Related papers: Improving sampling of binding free energy differen…
Achieving faster execution with shorter compilation time can enable further diversity and innovation in neural networks. However, the current paradigm of executing neural networks either relies on hand-optimized libraries, traditional…
Hybrid sequence models--combining Transformer and state-space model layers--seek to gain the expressive versatility of attention as well as the computational efficiency of state-space model layers. Despite burgeoning interest in hybrid…
We present a novel quantum circuit extraction scheme that tightly integrates graph-like ZX diagrams with hardware-adaptive routing. The method utilizes the degrees of freedom during the conversion from a ZX diagram to a quantum circuit…
We discuss theoretical models for the cooperative binding dynamics of ligands to substrates, such as dimeric motor proteins to microtubules or more extended macromolecules like tropomyosin to actin filaments. We study the effects of steric…
Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space one is then able to sample efficiently…
Finding and sampling multiple reaction channels for molecular transitions remains an important challenge in physical chemistry. Here we show that the weighted ensemble (WE) path sampling method can readily sample multiple channels. In a…
Coarse-graining (CG) enables molecular dynamics (MD) simulations of larger systems and longer timescales that are otherwise infeasible with atomistic models. Machine learning potentials (MLPs), with their capacity to capture many-body…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
More and more applications are adopting the charging topology of wireless power transmission. However, most wireless charging systems can not charge mobile devices which are moving in position while charging. Currently, many commercialized…
Optimization of strongly non-linear tightly coupled feeds attached to antennas is a challenging problem from a purely computational perspective. One can imagine that an optimization would (a) need to be in the time domain, and (b) has to be…
Transition interface sampling (TIS) and replica exchange TIS (RETIS) are powerful methods for computing rates of rare events inaccessible to straightforward molecular dynamics (MD) simulations. Path reweighting extends their output,…
Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this…
It has been well established that increasing scale in deep transformer networks leads to improved quality and performance. However, this increase in scale often comes with prohibitive increases in compute cost and inference latency. We…
We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations based on the Wang-Landau method. To demonstrate its advantages and general applicability for massively parallel simulations of complex systems, we…
Replica exchange (REX) is one of the most widely used enhanced sampling methodologies, yet its efficiency is limited by the requirement for a large number of intermediate temperature replicas. Here we present Generative Replica Exchange…
We study the problem of finding efficient sampling policies in an edge-based feedback system, where sensor samples are offloaded to a back-end server that processes them and generates feedback to a user. Sampling the system at maximum…
I propose an approximation scheme for asymptotically free field theories combining both weak coupling and strong coupling series. The weak coupling expansion is used to integrate the high frequency modes and the resulting low energy…
This paper presents a novel sampling scheme for masked non-autoregressive generative modeling. We identify the limitations of TimeVQVAE, MaskGIT, and Token-Critic in their sampling processes, and propose Enhanced Sampling Scheme (ESS) to…
This paper studies the optimal transmission switching (OTS) problem for power systems, where certain lines are fixed (uncontrollable) and the remaining ones are controllable via on/off switches. The goal is to identify a topology of the…
We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in…