相关论文: Peptide Conformational Equilibria Computed via a S…

The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making…

We introduce and implement a Monte Carlo scheme to study the equilibrium statistics of polymers in the globular phase. It is based on a model of "interacting elastic lattice polymers" and allows a sufficiently good sampling of long and…

We study the convergence to equilibrium of an underdamped Langevin equation that is controlled by a linear feedback force. Specifically, we are interested in sampling the possibly multimodal invariant probability distribution of a Langevin…

We propose a method to compute free-energy differences from nonadiabatic alchemical transformations using flow-based generative models. The method, nonadiabatic force matching, hinges on estimating the dissipation along an alchemical…

Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug-design. Current techniques suffer from being model specific,…

Computing phase diagrams of model systems is an essential part of computational condensed matter physics. In this paper we discuss in detail the interface pinning (IP) method for calculation of the Gibbs free energy difference between a…

We devise a hierarchy of computational algorithms to enumerate the microstates of a system comprising N independent, distinguishable particles. An important challenge is to cope with integers that increase exponentially with system size,…

This work investigates two physics-based models that simulate the non-linear partial differential algebraic equations describing an electric double layer supercapacitor. In one model the linear dependence between electrolyte concentration…

We present an algorithm to simulate the many-body depletion interaction between anisotropic colloids in an implicit way, integrating out the degrees of freedom of the depletants, which we treat as an ideal gas. Because the depletant…

We show that even though the Discontinuous Galerkin Spectral Element Method is stable for hyperbolic boundary-value problems, and the overset domain problem is well-posed in an appropriate norm, the energy of the approximation of the latter…

Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updating probabilities of the dihedral angles is defined, which…

Predicting observables in equilibrium states is a central yet notoriously hard question in quantum many-body systems. In the physically relevant thermodynamic limit, certain mathematical formulations of this task have even been shown to…

We present a new method to evaluate vibrational free energies of atomic systems without a priori specification of an interatomic potential. Our model-agnostic approach leverages descriptors, high-dimensional feature vectors of atomic…

We analyze a system of two colliding ultracold atoms under strong harmonic confinement from the viewpoint of quantum defect theory and formulate a generalized self-consistent method for determining the allowed energies. We also present two…

Interplay of Coulomb interaction energy, free ion entropy, and conformational elasticity is a fascinating aspect in polyelectrolytes (PEs). We develop a theory for complexation of two oppositely charged PEs, a process known to be the…

The stochastic differential equations for a model of dissipative particle dynamics, with both total energy and total momentum conservation at every time-step, are presented. The algorithm satisfies detailed balance as well as the…

Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…

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…

Stabilization of an underactuated mechanical system may be accomplished by energy shaping. Interconnection and damping assignment passivity-based control is an approach based on total energy shaping by assigning desired kinetic and…

The recently developed Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT) is investigated for a wide range of model parameters including the parameter m representing the chain length and the thermodynamic temperature T and…