Related papers: Configurational space continuity and free energy c…
In this work, I propose a statistical mechanical framework, for the evaluation of the free energy in molecular systems, by "deleting" all the molecules in a "single" step. The approach can be considered as the statistical mechanics…
We propose a new approach, "structure integration", enabling direct evaluation of configurational free energy for large systems. The present approach is based on the statistical information of lattice. Through first-principles-based…
Predictions of relative stabilities of (competing) molecular crystals are of great technological relevance, most notably for the pharmaceutical industry. However, they present a long-standing challenge for modeling, as often minuscule free…
We consider the steady state of an open system in which there is a flux of matter between two reservoirs at different chemical potentials. For a large system of size $N$, the probability of any macroscopic density profile $\rho(x)$ is…
Recently, we clarify connection of spatial constraint and equilibrium macroscopic properties in disordered states of classical system under the fixed composition; namely few special microscopic states, independent of constituent elements,…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…
The idea that possible configurations of a physical system can be represented as points in a multidimensional configuration space ${\cal C}$ is explored. The notion of spacetime, without ${\cal C}$, does not exist in this theory. Spacetime…
In this PhD thesis, we explore and apply methods inspired by the free energy principle to two important areas in machine learning and neuroscience. The free energy principle is a general mathematical theory of the necessary…
Powerspaces of directed spaces play an important role in modeling the semantics of nondeterministic functional programming languages. The notions of upper,lower and convex powerspace of a directed space are defined by the way of free…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
Defects determine many important properties and applications of materials, ranging from doping in semiconductors, to conductivity in mixed ionic-electronic conductors used in batteries, to active sites in catalysts. The theoretical…
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…
We propose a new Monte Carlo algorithm for the free energy calculation based on configuration space sampling. We implement this algorithm for Ising model. Comparison with the exact free energy shows an excellent agreement. We analyse the…
Trajectories provide dynamical information that is discarded in free energy calculations, for which we sought to design a scheme with the hope of saving cost for generating dynamical information. We first demonstrated that snapshots in a…
We consider a simple model to describe the widths of the mode locked intervals for the critical circle map. Using two different partitions of the rational numbers, based on Farey series and Farey tree levels respectively, we calculate the…
Maximizing the amount of work harvested from an environment is important for a wide variety of biological and technological processes, from energy-harvesting processes such as photosynthesisto energy storage systems such as fuels and…
Energy system models based on linear programming have been growing in size with the increasing need to model renewables with high spatial and temporal detail. Larger models lead to high computational requirements. Furthermore, seemingly…
Free energy calculation is critical in predictive tasks such as protein folding, docking and design. However, rigorous calculation of free energy change is prohibitively expensive in these practical applications. The minimum potential…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…
Quantum technologies are developing powerful tools to generate and manipulate coherent superpositions of different energy levels. Envisaging a new generation of energy-efficient quantum devices, here we explore how coherence can be…