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Numrering	Referens	Omslagsbild	Hitta
1.	Aidas, Kestutis, et al. (författare) The Dalton quantum chemistry program system 2014 Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 4:3, s. 269-284 Tidskriftsartikel (refereegranskat)abstract Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.
2.	Aquilante, Francesco, et al. (författare) MOLCAS-a software for multiconfigurational quantum chemistry calculations 2013 Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : Wiley. - 1759-0884 .- 1759-0876. ; 3:2, s. 143-149 Tidskriftsartikel (refereegranskat)abstract At variance, with most of the quantum chemistry software presently available, MOLCAS is a package that is specialized in multiconfigurational wave function theory (MC-WFT) rather than density functional theory (DFT). Given the much higher algorithmic complexity of MC-WFT versus DFT, an extraordinary effort needs to be made from the programming point of view to achieve state-of-the-art performance for large-scale calculations. In particular, a robust and efficient implementation of the Cholesky decomposition techniques for handling two-electron integrals has been developed which is unique to MOLCAS. Together with this 'Cholesky infrastructure', a powerful and multilayer graphical and scripting user interface is available, which is an essential ingredient for the setup of MC-WFT calculations. These two aspects of the MOLCAS software constitute the focus of the present report. (C) 2012 John Wiley & Sons, Ltd.
3.	Chakraborty, Pratip, et al. (författare) Time-resolved photoelectron spectroscopy via trajectory surface hopping 2024 Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 14:3 Forskningsöversikt (refereegranskat)abstract Time-resolved photoelectron spectroscopy is a powerful pump-probe technique which can probe nonadiabatic dynamics in molecules. Interpretation of the experimental signals however requires input from theoretical simulations. Advances in electronic structure theory, nonadiabatic dynamics, and theory to calculate the ionization yields, have enabled accurate simulation of time-resolved photoelectron spectra leading to successful applications of the technique. We review the basic theory and steps involved in calculating time-resolved photoelectron spectra, and highlight successful applications. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Theoretical and Physical Chemistry > Spectroscopy.
4.	Delcey, Mickael G, 1988- (författare) MultiPsi: A python-driven MCSCF program for photochemistry and spectroscopy simulations on modern HPC environments 2023 Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 13:6 Tidskriftsartikel (refereegranskat)abstract We present MultiPsi, an open-source MCSCF program for the calculation of ground and excited states properties of strongly correlated systems. The program currently implements a general MCSCF code with excited states available using either state-averaging or linear response. It is written in a highly modular fashion using Python/C++ which makes it well suited as a development platform, enabling easy prototyping of novel methods, and as a teaching tool using interactive notebooks. The code is also very efficient and designed for modern high-performance computing environments using hybrid OpenMP/MPI parallelization. This efficiency is demonstrated with the calculation of the CASSCF energy and linear response of a molecule with more than 700 atoms as well as a fully optimized conventional CI calculation on more than 400 billion determinants. This article is categorized under: Software > Quantum Chemistry Electronic Structure Theory > Ab Initio Electronic Structure Methods Theoretical and Physical Chemistry > Spectroscopy.
5.	Friedman, Ran (författare) Computational studies of protein–drug binding affinity changes upon mutations in the drug target 2022 Ingår i: WIREs Computational Molecular Science. - : John Wiley & Sons. - 1759-0876 .- 1759-0884. ; 12:1 Tidskriftsartikel (refereegranskat)abstract Mutations that lead to drug resistance limit the efficacy of antibiotics, antiviral drugs, targeted cancer therapies, and other treatments. Accurately calculating protein–drug binding affinity changes upon mutations in the drug target is of high interest as this can yield a better understanding into how such mutations drive drug-resistance, especially when the mutation in question does not directly interfere with binding of the drug. The main aim of this article is to provide an up-to-date reference on the computational tools that are available for the calculation of Gibbs energy (free energy) changes upon mutation, their strengths, and limitations. The methods that are discussed include free energy calculations (free energy perturbation, thermodynamic integration, multistate Bennett acceptance ratio), analysis of molecular dynamics simulations (linear interaction energy, molecular mechanics [MM]/Poisson–Boltzmann solvated area, and MM/generalized Born solvated area), and methods that involve quantum mechanical calculations (including QM/MM). The possibility to use machine learning is also introduced. Given that the benefit of accurately calculating binding affinity changes upon mutation depends on comparing calculated values with experimental measurements, a brief survey on experimental methods and observables is provided. Examples of computational studies that go beyond calculating the Gibbs energy changes are given. Factors that need to be addressed by the computational chemist and potential pitfalls are discussed at length.
6.	Herbst, Michael F., et al. (författare) adcc : A versatile toolkit for rapid development of algebraic-diagrammatic construction methods 2020 Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 10:6 Tidskriftsartikel (refereegranskat)abstract ADC-connect (adcc) is a hybrid python/C++ module for performing excited state calculations based on the algebraic-diagrammatic construction scheme for the polarization propagator (ADC). Key design goal is to restrict adcc to this single purpose and facilitate connection to external packages, for example, for obtaining the Hartree-Fock references, plotting spectra, or modeling solvents. Interfaces to four self-consistent field codes have already been implemented, namely pyscf, psi4, molsturm, and veloxchem. The computational workflow, including the numerical solvers, is implemented in python, whereas the working equations and other expensive expressions are done in C++. This equips adcc with adequate speed, making it a flexible toolkit for both rapid development of ADC-based computational spectroscopy methods as well as unusual computational workflows. This is demonstrated by three examples. Presently, ADC methods up to third order in perturbation theory are available in adcc, including the respective core-valence separation and spin-flip variants. Both restricted or unrestricted Hartree-Fock references can be employed.This article is categorized under: Software > Simulation Methods Electronic Structure Theory > Ab Initio Electronic Structure Methods Theoretical and Physical Chemistry > Spectroscopy Software > Quantum Chemistry
7.	Hu, Wei, et al. (författare) Theoretical modeling of surface and tip-enhanced Raman spectroscopies 2017 Ingår i: WIREs Computational Molecular Science. - : WILEY. - 1759-0876 .- 1759-0884. ; 7:2 Forskningsöversikt (refereegranskat)abstract Raman spectroscopy is a powerful technique in molecular science because of the ability of providing vibrational 'finger-print'. The developments of the surfaceenhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS) have significantly improved the detection sensitivity and efficiency. However, they also introduce complications for the spectral assignments, for which advanced theoretical modeling has played an important role. Here we summarize some of our recent progresses for SERS and TERS, which generally combine both solid-state physics and quantum chemistry methods with two different schemes, namely the cluster model and the periodic boundary condition (PBC) model. In the cluster model, direct Raman spectra calculations are performed for the cluster taken from the accurate PBC structure. For PBC model, we have developed a quasianalytical approach that enables us to calculate the Raman spectra of entire system. Under the TERS condition, the non-uniformity of plasmonic field in real space can drastically alter the interaction between the molecule and the light. By taking into account the local distributions of the plasmonic field, a new interaction Hamiltonian is constructed and applied to model the super-high-resolution Raman images of a single molecule. It shows that the resonant Raman images reflect the transition density between ground and excited states, which are generally vibrational insensitive. The nonresonant Raman images, on the other hand, allow to visualize the atomic movement of individual vibrational modes in real space. The inclusion of non-uniformity of plasmonic field provides ample opportunities to discover new physics and new applications in the future.
8.	Kamerlin, Shina C. L., 1981-, et al. (författare) The empirical valence bond model : theory and applications 2011 Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 1:1, s. 30-45 Tidskriftsartikel (refereegranskat)abstract Recent years have seen an explosion in computer power, allowing for the examination of ever more challenging problems. For instance, a recent simulation study, which was the first of its kind, was able to actually explore the dynamical nature of enzyme catalysis on a millisecond timescale (Pisliakov AV, Cao J, Kamerlin SCL, Warshel A. Proc Natl Acad Sci U S A 2009, 106:17359.), something that as recently as a year or two ago would have been considered impossible. However, the questions that need addressing are nevertheless very complex, and experimental approaches can unfortunately often be inconclusive (Åqvist J, Kolmodin K, Florián J, Warshel A, Chem Biol 1999, 6:R71.) in answering them. Therefore, it is essential to have an approach that is both reliable and able to capture complex systems in order to resolve long-standing controversies [particularly with regards to questions such as the origin of enzyme catalysis, where the relevant energy contributions cannot be separated without some computational models (Warshel A, Sharma PK, Kato M, Xiang Y, Liu H, Olsson MHM, Chem Rev 2006, 106:3210.)]. Herein, we will present the empirical valence bond (EVB) approach, which, at present, is arguably the most powerful tool for examining chemical reactivity in the condensed phase. We will illustrate the effectiveness of the EVB method when evaluating, for instance, catalytic effects and demonstrate that it is currently the optimal tool for elucidating challenging problems such as understanding the catalytic power of enzymes. Finally, the increasing appreciation of this approach can maybe best illustrated not only by its proliferation but also by attempts to capture its basic chemistry under a different name, as will be discussed in this work.
9.	Larsson, Per, 1972-, et al. (författare) Algorithm improvements for molecular dynamics simulations 2011 Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 1:1, s. 93-108 Tidskriftsartikel (refereegranskat)abstract High-performance implementations of molecular dynamics (MD) simulations play an important role in the study of macromolecules. Recent advances in both hardware and simulation software have extended the accessible time scales significantly, but the more complex algorithms used in many codes today occasionally make it difficult to understand the program flow and data structures without at least some knowledge about the underlying ideas used to improve performance. In this review, we discuss some of the currently most important areas of algorithm improvement to accelerate MD, including floating-point maths, techniques to accelerate nonbonded interactions, and methods to allow multiple or extended time steps. There is also a strong trend of increased parallelization on different levels, including both distributed memory domain decomposition, stream processing algorithms running, e. g., on graphics processing units hardware, and last but not least techniques to decouple simulations to enable massive parallelism on next-generation supercomputers or distributed computing. We describe some of the impacts these algorithms are having in current performance, and also how we believe they can be combined in the future.
10.	Pedersen, Thomas Bondo, et al. (författare) The versatility of the Cholesky decomposition in electronic structure theory 2024 Ingår i: WIREs Computational Molecular Science. - : John Wiley & Sons. - 1759-0876 .- 1759-0884. ; 14:1 Tidskriftsartikel (refereegranskat)abstract The resolution-of-the-identity (RI) or density fitting (DF) approximation for the electron repulsion integrals (ERIs) has become a standard component of accelerated and reduced-scaling implementations of first-principles Gaussian-type orbital electronic-structure methods. The Cholesky decomposition (CD) of the ERIs has also become increasingly deployed across quantum chemistry packages in the last decade, even though its early applications were mostly limited to high-accuracy methods such as coupled-cluster theory and multiconfigurational approaches. Starting with a summary of the basic theory underpinning both the CD and RI/DF approximations, thus underlining the extremely close relation of the CD and RI/DF techniques, we provide a brief and largely chronological review of the evolution of the CD approach from its birth in 1977 to its current state. In addition to being a purely numerical procedure for handling ERIs, thus providing robust and computationally efficient approximations to the exact ERIs that have been found increasingly useful on modern computer platforms, CD also offers highly accurate approaches for generating auxiliary basis sets for the RI/DF approximation on the fly due to the deep mathematical connection between the two approaches. In this review, we aim to provide a concise reference of the main techniques employed in various CD approaches in electronic structure theory, to exemplify the connection between the CD and RI/DF approaches, and to clarify the state of the art to guide new implementations of CD approaches across electronic structure programs.
11.	Poongavanam, Vasanthanathan, et al. (författare) Integrative approaches in HIV-1 non-nucleoside reverse transcriptase inhibitor design 2018 Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 8:1 Tidskriftsartikel (refereegranskat)abstract The design of inhibitors for human immunodeficiency virus type-1 reverse transcriptase (HIV-1 RT) is one of the most successful approaches for the treatment of HIV infections. Among the HIV-1 RT inhibitors, non-nucleoside reverse transcriptase inhibitors (NNRTIs) constitute a prominent drug class, which includes nevirapine, delavirdine, efavirenz, etravirine, and rilpivirine approved for clinical use. However, the efficiency of many of these drugs has been undermined by drug-resistant variants of HIV-1 RT, and it therefore becomes inevitable to design novel drugs to cope with resistance. Here, we discuss various drug design strategies, which include traditional medicinal chemistry, computational chemistry, and chemical biology approaches. In particular, computational modeling approaches, including machine learning, empirical descriptors-based, force-field, ab initio, and hybrid quantum mechanics/molecular mechanics-based methods are discussed in detail. We foresee that these methods will have a major impact on efforts to guide the design and discovery of the next generation of NNRTIs that combat RT multidrug resistance.
12.	Rehn, D. R., et al. (författare) Gator : A Python-driven program for spectroscopy simulations using correlated wave functions 2021 Ingår i: WIREs Computational Molecular Science. - : John Wiley and Sons Inc. - 1759-0876 .- 1759-0884. ; 11:6 Tidskriftsartikel (refereegranskat)abstract The Gator program has been developed for computational spectroscopy and calculations of molecular properties using real and complex propagators at the correlated level of wave function theory. Currently, the focus lies on methods based on the algebraic diagrammatic construction (ADC) scheme up to the third order of perturbation theory. An auxiliary Fock matrix-driven implementation of the second-order ADC method for excitation energies has been realized with an underlying hybrid MPI/OpenMP parallelization scheme suitable for execution in high-performance computing cluster environments. With a modular and object-oriented program structure written in a Python/C++ layered fashion, Gator additionally enables time-efficient prototyping of novel scientific approaches, as well as interactive notebook-driven training of students in quantum chemistry. This article is categorized under: Computer and Information Science > Computer Algorithms and Programming Electronic Structure Theory > Ab Initio Electronic Structure Methods Software > Quantum Chemistry.
13.	Reine, Simen, et al. (författare) Multi-electron Integrals 2012 Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 2:2, s. 290-303 Forskningsöversikt (refereegranskat)abstract This review presents techniques for the computation of multi-electron integrals over Cartesian and solid-harmonic Gaussian-type orbitals as used in standard electronic-structure investigations. The review goes through the basics for one- and two-electron integrals, discuss details of various two-electron integral evaluation schemes, approximative methods, techniques to compute multi-electron integrals for explicitly correlated methods, and property integrals.
14.	Rinkevicius, Zilvinas, et al. (författare) VeloxChem : A Python-driven density-functional theory program for spectroscopy simulations in high-performance computing environments 2019 Ingår i: WIREs Computational Molecular Science. - : Blackwell Publishing Inc.. - 1759-0876 .- 1759-0884. Tidskriftsartikel (refereegranskat)abstract An open-source program named VeloxChem has been developed for the calculation of electronic real and complex linear response functions at the levels of Hartree–Fock and Kohn–Sham density functional theories. With an object-oriented program structure written in a Python/C++ layered fashion, VeloxChem enables time-efficient prototyping of novel scientific approaches without sacrificing computational efficiency, so that molecular systems involving up to and beyond 500 second-row atoms (or some 10,000 contracted and in part diffuse Gaussian basis functions) can be routinely addressed. In addition, VeloxChem is equipped with a polarizable embedding scheme for the treatment of the classical electrostatic interactions with an environment that in turn is modeled by atomic site charges and polarizabilities. The underlying hybrid message passing interface (MPI)/open multiprocessing (OpenMP) parallelization scheme makes VeloxChem suitable for execution in high-performance computing cluster environments, showing even slightly beyond linear scaling for the Fock matrix construction with use of up to 16,384 central processing unit (CPU) cores. An efficient—with respect to convergence rate and overall computational cost—multifrequency/gradient complex linear response equation solver enables calculations not only of conventional spectra, such as visible/ultraviolet/X-ray electronic absorption and circular dichroism spectra, but also time-resolved linear response signals as due to ultra-short weak laser pulses. VeloxChem distributed under the GNU Lesser General Public License version 2.1 (LGPLv2.1) license and made available for download from the homepage https://veloxchem.org. This article is categorized under: Software > Quantum Chemistry Electronic Structure Theory > Density Functional Theory Theoretical and Physical Chemistry > Spectroscopy.
15.	Roca-Sanjuan, Daniel, et al. (författare) Multiconfiguration second-order perturbation theory approach to strong electron correlation in chemistry and photochemistry 2012 Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 2:4, s. 585-603 Forskningsöversikt (refereegranskat)abstract Rooted in the very fundamental aspects of many chemical phenomena, and for the majority of photochemistry, is the onset of strongly interacting electronic configurations. To describe this challenging regime of strong electron correlation, an extraordinary effort has been put forward by a young generation of scientists in the development of theories 'beyond' standard wave function and density functional models. Despite their encouraging results, a twenty-and-more-year old approach still stands as the gold standard for these problems: multiconfiguration second-order perturbation theory based on complete active space reference wave function (CASSCF/CASPT2). We will present here a brief overview of the CASSCF/CASPT2 computational protocol, and of its role in our understanding of chemical and photochemical processes.
16.	Seritan, S., et al. (författare) TeraChem : A graphical processing unit-accelerated electronic structure package for large-scale ab initio molecular dynamics 2020 Ingår i: WIREs Computational Molecular Science. - : Blackwell Publishing Inc.. - 1759-0876 .- 1759-0884. Tidskriftsartikel (refereegranskat)abstract TeraChem was born in 2008 with the goal of providing fast on-the-fly electronic structure calculations to facilitate ab initio molecular dynamics studies of large biochemical systems such as photoswitchable proteins and multichromophoric antenna complexes. Originally developed for videogaming applications, graphics processing units (GPUs) offered a low-cost parallel computer architecture that became more accessible for general-purpose GPU computing with the release of CUDA in 2007. The evaluation of the electron repulsion integrals (ERIs) is a major bottleneck in electronic structure codes and provides an attractive target for acceleration on GPUs. Thus, highly efficient routines for evaluation of and contractions between the ERIs and density matrices were implemented in TeraChem. Electronic structure methods were developed and implemented to leverage these integral contraction routines, resulting in the first quantum chemistry package designed from the ground up for GPUs. This GPU acceleration makes TeraChem capable of performing large-scale ground and excited state calculations in the gas and condensed phase. Today, TeraChem's speed forms the basis for a suite of quantum chemistry applications, including optimization and dynamics of proteins, automated and interactive chemical discovery tools, and large-scale nonadiabatic dynamics simulations. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Software > Quantum Chemistry Structure and Mechanism > Computational Biochemistry and Biophysics.
17.	Siegbahn, Per E. M., et al. (författare) The quantum chemical clusterapproach for modeling enzymereactions 2011 Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 1:3, s. 323-356 Tidskriftsartikel (refereegranskat)abstract This Overview describes the general concepts behind the quantum chemical clusterapproach formodeling enzyme active sites and reaction mechanisms. First, theunderlying density functional electronic structure method is briefly recapitulated.The cluster methodology is then discussed, including the important observationon the convergence of the solvation effects. The concepts are illustrated usingexamples from recent applications, such as the discrimination between differentreaction mechanisms in phosphotriesterase, the elucidation of origins of regioselectivityin the epoxide-opening reaction of haloalcohol dehalogenase, and finallythe use of the cluster methodology to establish the detailed structure of theoxygen-evolving complex in photosystem II.
18.	Singh, Deobrat, et al. (författare) Dimensionality effects in high-performance thermoelectric materials : Computational and experimental progress in energy harvesting applications 2022 Ingår i: WIREs Computational Molecular Science. - : John Wiley & Sons. - 1759-0876 .- 1759-0884. ; 12:1 Forskningsöversikt (refereegranskat)abstract Thermoelectric (TE) materials can be used in the conversion of heat to electricity and vice versa, which can enhance the efficiency of the fuel, in addition to supplying solid alternative energy in several applications in accumulating waste heat and, as a result, help to find new energy sources. Considering the current environment as well as the energy crisis, the TE modules are a need of the future. The present review focuses on the new strategies and approaches to achieve high-performance TE materials including materials improvement, structures, and geometry improvement and their applications. Controlling the carrier concentration and the band structures of materials is an effective way to optimize the electrical transport properties, while engineered nanostructures and engineering defects can immensely decrease the thermal conductivity and significantly improved the power factor. The present review gives a better understanding of how the theory is affecting the TE field.
19.	van der Spoel, David, et al. (författare) GROMACS-the road ahead 2011 Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 1:5, s. 710-715 Tidskriftsartikel (refereegranskat)abstract Molecular dynamics (MD) simulations form a powerful tool that is complementary to experiments and theory. They allow detailed investigations of both biological and chemical systems at the atomic level at timescales ranging from femtoseconds to milliseconds. Mechanisms and processes not accessible to experimental techniques can be followed in 'real time', and hypotheses based on experiments or theoretical arguments can be tested. Limits on the accuracy of results are mainly due to the physical models, the ratio of the complexity of the problem and the amount of computer time. Here, we review the state of the art in MD simulations with a focus on imminent challenges for the GROMACS (GROningen MAchine for Chemical Simulation) software. New hardware puts new requirements on software, while the breadth of applications and the amount of physical models implemented are increasing rapidly, highlighting shortcomings in the architecture of the programs. We sketch a road map for a popular scientific software package and discuss some of the choices to be made.
20.	Van der Spoel, David, et al. (författare) Quantitative predictions from molecular simulations using explicit or implicit interactions 2022 Ingår i: WIREs Computational Molecular Science. - : John Wiley & Sons. - 1759-0876 .- 1759-0884. ; 12:1 Forskningsöversikt (refereegranskat)abstract Equilibrium simulations of molecular systems allow to extract many physicochemical properties. Given an "accurate enough" model, a "large enough" simulation system and "long enough" simulations, such calculations should yield accurate predictions of properties that can be tested by experimental measurements. Non-equilibrium simulations can be used as a tool to obtain specific properties like viscosity or conductivity, but they have the drawback that in general only one property per simulation is produced. In addition, a range of methods is available for computing free energy differences. We here review the state of the art of using classical simulation models for generating quantitative predictions. Popular force fields have significant predictive power already but there is room for improvement. Bonded force potentials may need to be replaced by more accurate ones to better reproduce vibrational frequencies. Simplification of non-bonded force terms, such as cut-offs for electrostatic or dispersion interactions, should be avoided. Routine usage of force field methods will therefore require some tuning of parameters. Despite the extensive toolbox that is available for producing quantitative results, the computational cost of explicit solvent simulation is significant and therefore, approximate methods like implicit solvent models remain popular and are still being developed. Based on fundamental arguments as well as on examples of solvation free energies, host-guest complexation and non-covalent association of molecules in solution, we conclude that implicit solvents as well as algorithmic simplifications are most useful when validation using experimental data or rigorous theoretical treatments is possible.
21.	van Keulen, S. C., et al. (författare) Multiscale molecular simulations to investigate adenylyl cyclase-based signaling in the brain 2023 Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 13:1 Tidskriftsartikel (refereegranskat)abstract Adenylyl cyclases (ACs) play a key role in many signaling cascades. ACs catalyze the production of cyclic AMP from ATP and this function is stimulated or inhibited by the binding of their cognate stimulatory or inhibitory Gα subunits, respectively. Here we used simulation tools to uncover the molecular and subcellular mechanisms of AC function, with a focus on the AC5 isoform, extensively studied experimentally. First, quantum mechanical/molecular mechanical free energy simulations were used to investigate the enzymatic reaction and its changes upon point mutations. Next, molecular dynamics simulations were employed to assess the catalytic state in the presence or absence of Gα subunits. This led to the identification of an inactive state of the enzyme that is present whenever an inhibitory Gα is associated, independent of the presence of a stimulatory Gα. In addition, the use of coevolution-guided multiscale simulations revealed that the binding of Gα subunits reshapes the free-energy landscape of the AC5 enzyme by following the classical population-shift paradigm. Finally, Brownian dynamics simulations provided forward rate constants for the binding of Gα subunits to AC5, consistent with the ability of the protein to perform coincidence detection effectively. Our calculations also pointed to strong similarities between AC5 and other AC isoforms, including AC1 and AC6. Findings from the molecular simulations were used along with experimental data as constraints for systems biology modeling of a specific AC5-triggered neuronal cascade to investigate how the dynamics of downstream signaling depend on initial receptor activation.
22.	Wieczór, M., et al. (författare) Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research : A use case 2023 Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 13:1 Tidskriftsartikel (refereegranskat)abstract Exascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified the power of these simulation strategies with the work done by the HPC simulation community to fight Covid-19 pandemics. This article is categorized under: Data Science > Computer Algorithms and Programming Data Science > Databases and Expert Systems Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods.

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