Related papers: Approximating Free Energy and Committor Landscapes…
We address the problem of constructing accurate mathematical models of the dynamics of complex systems projected on a collective variable. To this aim we introduce a conceptually simple yet effective algorithm for estimating the parameters…
Biomolecular conformational transitions are usually modeled as barrier crossings in a free energy landscape. The transition paths connect two local free energy minima and transition path times (TPT) are the actual durations of the crossing…
This paper considers intelligent reflecting surface (IRS)-aided simultaneous wireless information and power transfer (SWIPT) in a multi-user multiple-input single-output (MISO) interference channel (IFC), where multiple transmitters (Txs)…
Popular methods for identifying transition paths between energy minima, such as the nudged elastic band and string methods, typically do not incorporate potential energy curvature information, leading to slow relaxation to the minimum…
Sampling techniques, such as t-wise interaction sampling are used to enable efficient testing for configurable systems. This is achieved by generating a small yet representative sample of configurations for a system, which circumvents…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
Computing reactive trajectories and free energy (FE) landscapes associated to rare event kinetics is key to understanding the dynamics of complex systems. The analysis of the FE surface on which the underlying dynamics takes place has…
We present an efficient algorithm for calculating the minimum energy path (MEP) and energy barriers between local minima on a multidimensional potential energy surface (PES). Such paths play a central role in the understanding of transition…
We study the forecasting problem for traffic with dynamic, possibly periodical, and joint spatial-temporal dependency between regions. Given the aggregated inflow and outflow traffic of regions in a city from time slots 0 to t-1, we predict…
Triply periodic minimal surfaces (TPMS) are a class of metamaterials with a variety of applications and well-known primitive morphologies. We present a new method for discovering novel microscale TPMS structures with exceptional…
Transition state (TS) searches are a critical bottleneck in computational studies of chemical reactivity, as accurately capturing complex phenomena like bond breaking and formation events requires repeated evaluations of expensive ab-initio…
We present a thermodynamic theory of plane coherent solid-solid interfaces in multicomponent systems subject to nonhydrostatic mechanical stresses. The interstitial and substitutional chemical components are treated separately using…
We describe a two-step approach for combining interactive molecular dynamics in virtual reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological processes at the molecular level. We refer to this combined…
This paper introduces a new paradigm of optimal path planning, i.e., passage-traversing optimal path planning (PTOPP), that optimizes paths' traversed passages for specified optimization objectives. In particular, PTOPP is utilized to find…
The minimum energy path (MEP) is the most probable transition path that connects two equilibrium states of a potential energy landscape. It has been widely used to study transition mechanisms as well as transition rates in the fields of…
Simulations of protein folding and protein association happen on timescales that are orders of magnitude larger than what can typically be covered in all-atom molecular dynamics simulations. Use of low-resolution models alleviates this…
The prediction of reaction pathways for solid-solid transformations remains a key challenge. Here, we develop a pathway sampling method via swarm intelligence and graph theory, and demonstrate that our PALLAS method is an effective tool to…
We have developed a numerical approach to compute real-time path integral expressions for quantum transport problems out of equilibrium. The scheme is based on a deterministic iterative summation of the path integral (ISPI) for the…
Transition Voltage Spectroscopy (TVS) has been proposed as a tool to analyze charge transport through molecular junctions. We extend TVS to Au-vacuum-Au junctions and study the distance dependence of the transition voltage V_t(d) for clean…
This paper introduces a systematic approach to address the topological path identification (TPI) problem in power distribution networks. Our approach starts by listing the DSO's raw information coming from several sources. The raw…