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There is a growing mechanics literature concerning the macroscopic properties of mechanism-based mechanical metamaterials. This amounts mathematically to a homogenization problem involving nonlinear elasticity. A key goal is to identify the…
It has been a long challenge to analytically construct the quantitative temperature-dependent multi-well free-energy landscape over the space of order parameters describing phase transitions and associated critical phenomena. Here we…
We present a calculation of the change of free energy of a solid surface upon bending of the solid. It is based on extracting the surface stress through a molecular dynamics simulation of a bent slab by using a generalized stress theorem…
One of the challenging problems in the condensed matter physics is to understand the quantum many-body systems, especially, their physical mechanisms behind. Since there are only a few complete analytical solutions of these systems, several…
Metasurfaces have shown promising potentials in shaping optical wavefronts while remaining compact compared to bulky geometric optics devices. Design of meta-atoms, the fundamental building blocks of metasurfaces, relies on trial-and-error…
We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and…
This Perspective describes current computational efforts in the field of simulating photodynamics of transition metal complexes. We present the typical workflows and feature the strengths and limitations of the different contemporary…
Controlling polymorphism in molecular crystals is crucial in the pharmaceutical, dye, and pesticide industries. However, its theoretical description is extremely challenging, due to the associated long timescales ($ > 1 \, \mu s$). We…
A new approach for efficiently exploring the configuration space and computing the free energy of large atomic and molecular systems is proposed, motivated by an analogy with reinforcement learning. There are two major components in this…
We introduce a meshfree collocation framework to model the phase change from liquid to vapor at or above the boiling point. While typical vaporization or boiling simulations focus on the vaporization from the bulk of the fluid, here we…
As one approaches the continuum limit, $QCD$ systems, investigated via numerical simulations, remain trapped in sectors of field space with fixed topological charge. As a consequence the numerical studies of physical quantities may give…
Matrix element reweighting is a powerful experimental technique widely employed to maximize the amount of information that can be extracted from a collider data set. We present a procedure that allows to automatically evaluate the weights…
The recently introduced nested sampling algorithm allows the direct and efficient calculation of the partition function of atomistic systems. We demonstrate its applicability to condensed phase systems with periodic boundary conditions by…
Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production…
Zn(imidazolate)$_2$ metal-organic frameworks (MOFs) exhibit a remarkable degree of polymorphism. Because of their promising industrial applications, many research groups have investigated phase transitions, phase diagram and relative…
We present a novel phase-field model development capability in the open source MOOSE finite element framework. This facility is based on the 'modular free energy' approach in which the phase-field equations are implemented in a general form…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
We examine the phase space structures that govern reaction dynamics in the absence of critical points on the potential energy surface. We show that in the vicinity of hyperbolic invariant tori it is possible to define phase space dividing…
Path sampling approaches have become invaluable tools to explore the mechanisms and dynamics of so-called rare events that are characterized by transitions between metastable states separated by sizeable free energy barriers. Their…
Free energy sampling methods allow studying the full dynamics of activated processes. Unfortunately, the affordable accuracy of the potential describing the energy and forces of the system is usually rather low. Here we introduce a new…