Journal of Chemical Physics最新文献

We present a novel route to constructing cost-efficient semi-empirical approximations for the non-additive kinetic energy in subsystem density functional theory. The developed methodology is based on the use of Slater determinants composed of non-orthogonal Kohn-Sham-like orbitals for the evaluation of kinetic energy expectation values and the expansion of the inverse molecular-orbital overlap matrix into a Neumann series. By applying these techniques, we derived and implemented a series of orbital-dependent approximations for the non-additive kinetic energy, which are employed self-consistently. Our proof-of-principle computations demonstrated quantitatively correct results for potential energy curves and electron densities and hinted on the applicability of the introduced empirical parameters to different types of molecular systems and intermolecular interactions. Therefore, we conclude that the presented study is an important step toward constructing accurate and efficient orbital-dependent approximations for the non-additive kinetic energy applicable to large molecular systems.

Chromatin loop formation plays a crucial role in 3D genome interactions, with misfolding potentially leading to irregular gene expression and various diseases. While experimental tools such as Hi-C have advanced our understanding of genome interactions, the biophysical principles underlying chromatin loop formation remain elusive. This review examines computational approaches to chromatin folding, focusing on polymer models that elucidate chromatin loop mechanics. We discuss three key models: (1) the multi-loop-subcompartment model, which investigates the structural effects of loops on chromatin conformation; (2) the strings and binders switch model, capturing thermodynamic chromatin aggregation; and (3) the loop extrusion model, revealing the role of structural maintenance of chromosome complexes. In addition, we explore advanced models that address chromatin clustering heterogeneity in biological processes and disease progression. The review concludes with an outlook on open questions and current trends in chromatin loop formation and genome interactions, emphasizing the physical and computational challenges in the field.

Templated copolymerization, in which information stored in the sequence of a heteropolymer template is copied into another polymer product, is the mechanism behind all known methods of genetic information transfer. A key aspect of templated copolymerization is the eventual detachment of the product from the template. A second key feature of natural biochemical systems is that the template-binding free energies of both correctly matched and incorrect monomers are heterogeneous. Previous work has considered the thermodynamic consequences of detachment and the consequences of heterogeneity for polymerization speed and accuracy, but the interplay of both separation and heterogeneity remains unexplored. In this work, we investigate a minimal model of templated copying that simultaneously incorporates both detachment from behind the leading edge of the growing copy and heterogeneous interactions. We first extend existing coarse-graining methods for models of polymerization to allow for heterogeneous interactions. We then show that heterogeneous copying systems with explicit detachment do not exhibit the subdiffusive behavior observed in the absence of detachment when near equilibrium. Next, we show that heterogeneity in correct monomer interactions tends to result in slower, less accurate copying, while heterogeneity in incorrect monomer interactions tends to result in faster, more accurate copying, due to an increased roughness in the free energy landscape of either correct or incorrect monomer pairs. Finally, we show that heterogeneity can improve on known thermodynamic efficiencies of homogeneous copying, but these increased thermodynamic efficiencies do not always translate to increased efficiencies of information transfer.

Second-order Møller-Plesset perturbation theory is well-known as a computationally inexpensive approach to the electron correlation problem that is size-consistent with a size-consistent reference but fails to be regular. On the other hand, the less well-known many-body version of Brillouin-Wigner perturbation theory has the reverse properties: it is regular but fails to be size-consistent when used with the standard MP partitioning. Consequently, its widespread use remains limited. In this work, we analyze the ways in which it is possible to use alternative non-MP partitions of the Hamiltonian to yield variants of BW2 that are size-consistent as well as regular. We show that there is a vast space of such BW2 theories and also show that it is possible to define a repartitioned BW2 theory from the ground state density alone, which regenerates the exact correlation energy. We also provide a general recipe for deriving regular, size-consistent, and size-extensive partitions from physically meaningful components, and we apply the result to small model systems. The scope of these results appears to further set the stage for a revival of BW2 in quantum chemistry.

The catalytic activities of high-spin small Fe(III) oxides have been investigated for efficient hydrogen production through ammonia decomposition, using the artificial force induced reaction method within the framework of density functional theory with the B3LYP hybrid exchange-correlation functional. Our results reveal that the adsorption free energy of NH3 on (Fe2O3)n (n = 1-4) decreases with increasing cluster size up to n = 3, followed by a slight increase at n = 4. The strongest NH3 adsorption energy, 28.55 kcal/mol, was found for Fe2O3, where NH3 interacts with a two-coordinated Fe site, forming an Fe-N bond with a length of 2.11 Å. A comparative analysis of NH3 dehydrogenation and H2 formation on various Fe(III) oxide sizes identifies the rate-determining steps for each reaction. We found that the rate-determining step for the full NH3 dehydrogenation on (Fe2O3)n (n = 1-4) is size-dependent, with the NH* → N* + H* reaction acting as the limiting step for n = 1-3. In addition, our findings indicate that H2 formation is favored following the partial decomposition of NH3 on Fe(III) oxides.

The Generalized Langevin Equation has been successfully used to model and understand the conformational dynamics of molecules in solution. However, recent works have demonstrated that, in these kinds of applications, the usual fluctuation-dissipation relation connecting the statistics of the random force to the memory kernel could contain a cross-correlation term. In this work, we systematically explore the origins of this cross-correlation term and argue that it plays a role, particularly in the folding dynamics of biopolymers. Finally, we propose an approximation for the cross-correlation term within the usual fluctuation-dissipation relation.

The electron structure of the NixTiSe2 system has been studied by the electromotive force (EMF) method in Cu|Cu+|NixTiSe2 and Na|Na+|NixTiSe2 electrochemical cells. Two critical transitions have been found in this system at x = 0.25 and x = 0.35. At these compositions, a change in the nature of the chemical bond of nickel with its local environment occurs. The simple and useful EMF method has been applied as the instrument to study features of electron structure. A comparative analysis of critical points in the electronic structure of the MexTiSe2 (Me = Fe, Co, Ni) intercalate compounds was carried out.

We present optimal control methods for the optimization of periodic pulsed dynamic nuclear polarization (DNP) sequences. Specifically, we address the challenge of the optimization of a basic and repeated pulse sequence element which, apart from being easily adaptable to spin systems with different coupling interaction sizes, also proves beneficial in terms of performance. It is demonstrated that matrix power and matrix logarithm functions combined with an auxiliary matrix formalism can be used to derive expressions for gradient ascent pulse engineering (GRAPE) optimization. We illustrate how different implementations provide effective and intuitive control of DNP experiments by tailoring the effective Hamiltonian governing polarization transfer and, in this manner, addressing some of the limitations of prevailing optimal control based pulse design strategies.

Reverse nonequilibrium molecular dynamics (RNEMD) simulations impose a flux by swapping the velocities of two particles. This method allows for the calculation of transport coefficients, such as thermal conductivity and viscosity. The relation between the induced fluxes and the control parameters of RNEMD (such as the time interval between successive swap events) is not clear. Thus, trial-and-error is required to realize the desired fluxes in RNEMD simulations. In this study, we develop a theoretical framework using extreme value statistics to estimate the relation between the time interval and the resulting induced fluxes. Our RNEMD simulations, conducted with varying time intervals, confirm that the theoretical predictions are quantitatively consistent with the simulation results when the time interval exceeds the momentum relaxation time. Our RNEMD simulations also show that our theoretical predictions, which are valid for a large number of particles for swap candidates, work well even for a relatively small number of particles for swap candidates. These findings demonstrate that the induced fluxes can be reliably estimated, providing a valuable tool for selecting appropriate RNEMD parameters for simulations.

We introduce an alternative route to quasiparticle self-consistent GW calculations (qsGW) on the basis of a joint approximate diagonalization of the one-body GW Green's functions G(εnQP) taken at the input quasiparticle energies. Such an approach allows working with the full dynamical self-energy, without approximating the latter by a symmetrized static form as in the standard qsGW scheme. Calculations on the GW100 molecular test set lead, nevertheless, to a good agreement, at the 60 meV mean-absolute-error accuracy on the ionization potential, with respect to the conventional qsGW approach. We show further that constructing the density matrix from the full Green's function as in the fully self-consistent scGW scheme, and not from the occupied quasiparticle one-body orbitals, allows obtaining a scheme intermediate between the qsGW and scGW approaches, closer to coupled-cluster reference values.