相关论文: Direct evaluation of free energy for large system …
We investigate connections between the continuum and atomistic descriptions of deformable crystals, using certain interesting results from number theory. The energy of a deformed crystal is calculated in the context of a lattice model with…
We present a theoretical first-principles method to calculate the free energy of a magnetic system in its high-temperature paramagnetic phase, including vibrational, electronic, and magnetic contributions. The method for calculating free…
Self-assembly kinetics is usually described by approaches which assume that the shape of the aggregates has a definite form (e.g., spherical, cylindrical, cubic, etc), however that is unlikely to be the case in many finite-sized…
Lattice structures have great potential for several application fields ranging from medical and tissue engineering to aeronautical one. Their development is further speeded up by the continuing advances in additive manufacturing…
We introduce a {\it lattice} version of the Calogero Sutherland model adapted to describe $1/d^2$ pairwise interacting steps with discrete positions on a vicinal surface. The configurational free energy is obtained within a transfer matrix…
Quantum algorithms are well-suited to calculate estimates of the energy spectra for spin lattice systems. These algorithms are based on the efficient calculation of the discrete Fourier components of the density of states. The efficiency of…
The thesis consists of two projects. In the first project, we present a software that analyses RNA secondary structures and compares them. The goal of this software is to find the differences between two secondary structures (experimental…
In a previous work, the n-vicinity method for approximate calculation of the partition function of a spin system was proposed. The equation of state was obtained in the most general form. In the present paper, we analyze the applicability…
A fluctuation relation, which is an extended form of the Jarzynski equality, is introduced and discussed. We show how to apply this relation in order to evaluate the free energy landscape of simple systems. These systems are manipulated by…
The thermodynamics for a system with given temperature, density, and volume is described by the Canonical ensemble. The thermodynamics for a corresponding system with the same temperature, volume, and average density is described by the…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Numerical methods are used to examine the thermodynamic characteristics of the two-dimensional Ising model as a function of the number of spins N. Onsager's solution is generalized to a finite-size lattice, and experimentally validated…
To study martensitic phase transformation we use a micromechanical model based on statistical mechanics. Employing lattice Monte-Carlo simulations and realistic material properties for shape-memory alloys (SMA), we investigate the combined…
It is possible to formulate the thermodynamics of a glass forming system in terms of the properties of inherent structures, which correspond to the minima of the potential energy and build up the potential energy landscape in the…
The energies of a pair of strongly-interacting subsystems with arbitrary noninteger charges are examined from closed and open system perspectives. An ensemble representation of the charge dependence is derived, valid at all interaction…
We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on \emph{ab initio} molecular dynamics followed by a mapping onto a model…
A new theoretical approach is described for the inverse self-assembly problem, i.e., the reconstruction of the interparticle interaction from a given structure. This theory is based on the variational principle for the functional that is…
We propose a scheme for {\it ab initio} configurational sampling in multicomponent crystalline solids using Behler-Parinello type neural network potentials (NNPs) in an unconventional way: the NNPs are trained to predict the energies of…
Here we present an approximate analytical theory for the relationship between a protein structure's contact matrix and the shape of its energy spectrum in amino acid sequence space. We demonstrate a dependence of the number of sequences of…
We study the effect of random on-site energies on the critical temperature of a non-interacting Bose gas on a lattice. In our derivation the on-site energies are distributed according a Gaussian probability distribution function having…