| 1. |
|
|
| 2. |
- Silanteva, I. A., et al.
(författare)
-
Equilibrium properties of 3-arm star-shaped polyions : an entropic sampling Monte Carlo study
- 2017
-
Ingår i: Nanosystems: Physics, Chemistry, Mathematics. - : ITMO University. - 2220-8054. ; 8:1, s. 108-120
-
Tidskriftsartikel (refereegranskat)abstract
- The entropic sampling Monte Carlo method within Wang-Landau algorithm is applied to investigate properties of a lattice model of strongly charged flexible 3-arm star-shaped polyelectrolyte. The density of states is calculated, from which the canonical properties of the system in a wide temperature range are obtained by simple integration. The effects of the arm length and the short-range monomer-monomer potential on the thermal and structural properties of star polyions are studied. We calculate such characteristics as mean square radius of gyration and its components, the radius vector of the center of mass, components of the tensor of inertia and parameters characterizing the shape of the polyion. In this work, we focus on how these characteristics are influenced by the change of the reduced temperature which, within the considered model, is a parameter combining the effect of real temperature, linear charge density and solvent dielectric permittivity. The coil-globule transition is observed in most of the considered cases, and for the polyions with the longest length of arms ( 24), the transition from a liquid globule to a solid-like state is observed. Comparison of polyelectrolyte models with neutral ones is given.
|
|
| 3. |
|
|
| 4. |
- Vorontsov-Velyaminov, P. N., et al.
(författare)
-
Calculation of Canonical Properties and Excited States by Path Integral Numerical Methods
- 2011
-
Ingår i: Contributions to Plasma Physics. - : Wiley. - 0863-1042 .- 1521-3986. ; 51:4, s. 382-385
-
Tidskriftsartikel (refereegranskat)abstract
- Path integral Monte Carlo method in the expanded ensemble is used for calculation of the ratio of partition functions for different classes of permutations treating the problem of several interacting identical particles (fermions) in an external field. Wang-Landau algorithm is used for adjustment of balancing factors. For systems consisting of greater than two number of particles we propose an advanced variant of our approach which implies calculation of the ratio of positive and negative contributions to the partition function. Densities and energies of the sequence of excited states starting from the ground state for a system of non interacting quantum particles are calculated in turn, one by one, by means of considering systems with artificially excluded lowest energy levels and further obtaining of the ground state of each next system constructed in this way. The idea of evaluation of densities of excited states for a quantum system with interparticle interaction by evaluating density difference between systems of different number of noninteracting Fermi-copies of the system of interest is realized in terms of cyclic expansion formalism for a simple 2D system of two spinless fermions interacting via Coulomb repulsion.
|
|
| 5. |
- B. Brant Carvalho, Paulo H., et al.
(författare)
-
Exploring High-Pressure Transformations in Low-Z (H2, Ne) Hydrates at Low Temperatures
- 2022
-
Ingår i: Crystals. - : MDPI AG. - 2073-4352. ; 12:1
-
Tidskriftsartikel (refereegranskat)abstract
- The high pressure structural behavior of H-2 and Ne clathrate hydrates with approximate composition H-2/Ne center dot~4H(2)O and featuring cubic structure II (CS-II) was investigated by neutron powder diffraction using the deuterated analogues at ~95 K. CS-II hydrogen hydrate transforms gradually to isocompositional C-1 phase (filled ice II) at around 1.1 GPa but may be metastably retained up to 2.2 GPa. Above 3 GPa a gradual decomposition into C-2 phase (H-2 center dot H2O, filled ice I-c) and ice VIII' takes place. Upon heating to 200 K the CS-II to C-1 transition completes instantly whereas C-1 decomposition appears sluggish also at 200 K. C-1 was observed metastably up to 8 GPa. At 95 K C-1 and C-2 hydrogen hydrate can be retained below 1 GPa and yield ice II and ice I-c, respectively, upon complete release of pressure. In contrast, CS-II neon hydrate undergoes pressure-induced amorphization at 1.9 GPa, thus following the general trend for noble gas clathrate hydrates. Upon heating to 200 K amorphous Ne hydrate crystallizes as a mixture of previously unreported C-2 hydrate and ice VIII'.
|
|
| 6. |
- B. Brant Carvalho, Paulo H., 1990-, et al.
(författare)
-
Neutron scattering study of polyamorphic THF·17(H2O) : toward a generalized picture of amorphous states and structures derived from clathrate hydrates
- 2023
-
Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 25:21, s. 14981-14991
-
Tidskriftsartikel (refereegranskat)abstract
- From crystalline tetrahydrofuran clathrate hydrate, THF-CH (THF·17H2O, cubic structure II), three distinct polyamorphs can be derived. First, THF-CH undergoes pressure-induced amorphization when pressurized to 1.3 GPa in the temperature range 77-140 K to a form which, in analogy to pure ice, may be called high-density amorphous (HDA). Second, HDA can be converted to a densified form, VHDA, upon heat-cycling at 1.8 GPa to 180 K. Decompression of VHDA to atmospheric pressure below 130 K produces the third form, recovered amorphous (RA). Results from neutron scattering experiments and molecular dynamics simulations provide a generalized picture of the structure of amorphous THF hydrates with respect to crystalline THF-CH and liquid THF·17H2O solution (∼2.5 M). Although fully amorphous, HDA is heterogeneous with two length scales for water-water correlations (less dense local water structure) and guest-water correlations (denser THF hydration structure). The hydration structure of THF is influenced by guest-host hydrogen bonding. THF molecules maintain a quasiregular array, reminiscent of the crystalline state, and their hydration structure (out to 5 Å) constitutes ∼23H2O. The local water structure in HDA is reminiscent of pure HDA-ice featuring 5-coordinated H2O. In VHDA, the hydration structure of HDA is maintained but the local water structure is densified and resembles pure VHDA-ice with 6-coordinated H2O. The hydration structure of THF in RA constitutes ∼18 H2O molecules and the water structure corresponds to a strictly 4-coordinated network, as in the liquid. Both VHDA and RA can be considered as homogeneous.
|
|
| 7. |
- B. Brant Carvalho, Paulo H., et al.
(författare)
-
Pressure-induced amorphization of noble gas clathrate hydrates
- 2021
-
Ingår i: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 103:6
-
Tidskriftsartikel (refereegranskat)abstract
- The high-pressure structural behavior of the noble gas (Ng) clathrate hydrates Ar center dot 6.5 H2O and Xe center dot 7.2 H2O featuring cubic structures II and I, respectively, was investigated by neutron powder diffraction (using the deuterated analogues) at 95 K. Both hydrates undergo pressure-induced amorphization (PIA), indicated by the disappearance of Bragg diffraction peaks, but at rather different pressures, at 1.4 and above 4.0 GPa, respectively. Amorphous Ar hydrate can be recovered to ambient pressure when annealed at >1.5 GPa and 170 K and is thermally stable up to 120 K. In contrast, it was impossible to retain amorphous Xe hydrate at pressures below 3 GPa. Molecular dynamics (MD) simulations were used to obtain general insight into PIA of Ng hydrates, from Ne to Xe. Without a guest species, both cubic clathrate structures amorphize at 1.2 GPa, which is very similar to hexagonal ice. Filling of large-sized H cages does not provide stability toward amorphization for structure II, whereas filled small-sized dodecahedral D cages shift PIA successively to higher pressures with increasing size of the Ng guest. For structure I, filling of both kinds of cages, large-sized T and small-sized D, acts to stabilize in a cooperative fashion. Xe hydrate represents a special case. In MD, disordering of the guest hydration structure is already seen at around 2.5 GPa. However, the different coordination numbers of the two types of guests in the crystalline cage structure are preserved, and the state is shown to produce a Bragg diffraction pattern. The experimentally observed diffraction up to 4 GPa is attributed to this semicrystalline state.
|
|
| 8. |
- B. Brant Carvalho, Paulo H., et al.
(författare)
-
Structural investigation of three distinct amorphous forms of Ar hydrate
- 2021
-
Ingår i: RSC Advances. - : Royal Society of Chemistry. - 2046-2069. ; 11:49, s. 30744-30754
-
Tidskriftsartikel (refereegranskat)abstract
- Three amorphous forms of Ar hydrate were produced using the crystalline clathrate hydrate Ar·6.5H2O (structure II, Fd3m, a ≈ 17.1 Å) as a precursor and structurally characterized by a combination of isotope substitution (36Ar) neutron diffraction and molecular dynamics (MD) simulations. The first form followed from the pressure-induced amorphization of the precursor at 1.5 GPa at 95 K and the second from isobaric annealing at 2 GPa and subsequent cooling back to 95 K. In analogy to amorphous ice, these amorphs are termed high-density amorphous (HDA) and very-high-density amorphous (VHDA), respectively. The third amorph (recovered amorphous, RA) was obtained when recovering VHDA to ambient pressure (at 95 K). The three amorphs have distinctly different structures. In HDA the distinction of the original two crystallographically different Ar guests is maintained as differently dense Ar–water hydration structures, which expresses itself in a split first diffraction peak in the neutron structure factor function. Relaxation of the local water structure during annealing produces a homogeneous hydration environment around Ar, which is accompanied with a densification by about 3%. Upon pressure release the homogeneous amorphous structure undergoes expansion by about 21%. Both VHDA and RA can be considered frozen solutions of immiscible Ar and water in which in average 15 and 11 water molecules, respectively, coordinate Ar out to 4 Å. The local water structures of HDA and VHDA Ar hydrates show some analogy to those of the corresponding amorphous ices, featuring H2O molecules in 5- and 6-fold coordination with neighboring molecules. However, they are considerably less dense. Most similarity is seen between RA and low density amorphous ice (LDA), which both feature strictly 4-coordinated H2O networks. It is inferred that, depending on the kind of clathrate structure and occupancy of cages, amorphous states produced from clathrate hydrates display variable local water structures.
|
|
| 9. |
- Barros Brant Carvalho, Paulo Henrique, et al.
(författare)
-
Neutron scattering study of polyamorphic THF ∙ (H2O)17 – toward a generalized picture of amorphous states and structures derived from clathrate hydrates
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- From crystalline tetrahydrofuran clathrate hydrate, THF-CH (THF ∙ 17H2O, cubic structure II), three distinct polyamorphs can be derived. First, THF-CH undergoes pressure-induced amorphization when pressurized to 1.3 GPa in the temperature range 77–140 K to a form which, in analogy to pure ice, may be called high-density amorphous (HDA). Second, HDA can be converted to a densified form, very-HDA (VHDA), upon heat-cycling at 1.8 GPa to 180 K. Decompression of VHDA to atmospheric pressure below 130 K produces the third, recovered amorphous (RA) form. Results from a compilation of neutron scattering experiments and molecular dynamics simulations provide a generalized picture of the structure of amorphous THF hydrates with respect to crystalline THF-CH and liquid THF ∙ 17H2O solution (~2.5 M). The calculated density of (only in situ observable) HDA and VHDA at 2 GPa and 130 K is 1.287 and 1.328 g/cm3, respectively, whereas that of RA (at 1 atm) is 1.081 g/cm3. Although fully amorphous, HDA is heterogeneous with two length scales for water-water correlations (less dense local water structure) and guest-water correlations (denser THF hydration structure). The hydration structure of THF is influenced by guest-host hydrogen bonding. THF molecules maintain a quasiregular array, reminiscent of the crystalline state, and their hydration structure (out to 5 Å) constitutes ~23 H2O. The local water structure in HDA is reminiscent of pure HDA-ice, featuring 5-coordinated H2O. In VHDA, this structure is maintained but the local water structure is densified to resemble pure VHDA-ice with 6-coordinated H2O. The hydration structure of THF in RA constitutes ~18 H2O and the water structure corresponds to a strictly 4-coordinated network, as in the liquid. Both VHDA and RA can be considered as homogeneous, solid solutions of THF and water. The local water structure of water-rich (1:17) amorphous CHs resembles most that of the corresponding amorphous water ices when compared to guest-rich CHs, e.g., Ar ∙ ~6H2O. The proposed significance of different contributions of water local environments presents a simple view to justify neutron structure factor features.
|
|
| 10. |
- Jämbeck, Joakim P. M., 1986-, et al.
(författare)
-
Molecular Dynamics Studies of Liposomes as Carriers for Photosensitizing Drugs : Development, Validation, and Simulations with a Coarse-Grained Model
- 2014
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 10:1, s. 5-13
-
Tidskriftsartikel (refereegranskat)abstract
- Liposomes are proposed as drug delivery systems and can in principle be designed so as to cohere with specific tissue types or local environments. However, little detail is known about the exact mechanisms for drug delivery and the distributions of drug molecules inside the lipid carrier. In the current work, a coarse-grained (CG) liposome model is developed, consisting of over 2500 lipids, with varying degrees of drug loading. For the drug molecule, we chose hypericin, a natural compound proposed for use in photodynamic therapy, for which a CG model was derived and benchmarked against corresponding atomistic membrane bilayer model simulations. Liposomes with 21-84 hypericin molecules were generated and subjected to 10 microsecond simulations. Distribution of the hypericins, their orientations within the lipid bilayer, and the potential of mean force for transferring a hypericin molecule from the interior aqueous droplet through the liposome bilayer are reported herein.
|
|
