相关论文: Accelerating flux balance calculations in genome-s…

Neural networks have been successfully applied in various resource-constrained edge devices, where usually central processing units (CPUs) instead of graphics processing units exist due to limited power availability. State-of-the-art…

We present TTCF4LAMMPS, a toolkit for performing non-equilibrium molecular dynamics (NEMD) simulations to study fluid behaviour at low shear rates using the LAMMPS software. By combining direct NEMD simulations and the transient-time…

Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the timescales necessary to capture the structural evolution…

An effective way to improve energy efficiency is to throttle hardware resources to meet a certain performance target, specified as a QoS constraint, associated with all applications running on a multicore system. Prior art has proposed…

In the simulation of biological molecules, it is customary to impose constraints on the fastest degrees of freedom to increase the time step. The evaluation of the involved constraint forces must be performed in an efficient manner, for…

Learning formulas in Linear Temporal Logic (LTLf) from finite traces is a fundamental research problem which has found applications in artificial intelligence, software engineering, programming languages, formal methods, control of…

We develop a central limit theorem (CLT) for a non-parametric estimator of the transition matrices in controlled Markov chains (CMCs) with finite state-action spaces. Our results establish precise conditions on the logging policy under…

Model reduction is a central topic in systems biology and dynamical systems theory, for reducing the complexity of detailed models, finding important parameters, and developing multi-scale models for instance. While perturbation theory is a…

Metabolic pathways are fundamental maps in biochemistry that detail how molecules are transformed through various reactions. The complexity of metabolic network, where a single compound can play a part in multiple pathways, poses a…

This paper presents a convex reformulation of a nonlinear constrained optimization problem for Markov decision processes, and applies the technical findings to optimal control problems for an ensemble of thermostatically controlled loads…

Model Predictive Control (MPC) is a successful control methodology, which is applied to increasingly complex systems. However, real-time feasibility of MPC can be challenging for complex systems, certainly when an (extremely) large number…

The methodology named LIFE (Linear-in-Flux-Expressions) was developed with the purpose of simulating and analyzing large metabolic systems. With LIFE, the number of model parameters is reduced by accounting for correlations among the…

Despite the enormous success of Hamiltonian Monte Carlo and related Markov Chain Monte Carlo (MCMC) methods, sampling often still represents the computational bottleneck in scientific applications. Availability of parallel resources can…

Background: A classical problem in metabolic design is to maximize the production of desired compound in a given chemical reaction network by appropriately directing the mass flow through the network. Computationally, this problem is…

A Topological examination of phospholipid dynamics in the Far from Equilibrium state has demonstrated that metabolically active cells use waste heat to generate spatially patterned membrane flows by forced convection and shear. This paper…

Large-scale machine learning and data mining applications require computer systems to perform massive matrix-vector and matrix-matrix multiplication operations that need to be parallelized across multiple nodes. The presence of straggling…

Flexible loads, e.g. thermostatically controlled loads (TCLs), are technically feasible to participate in demand response (DR) programs. On the other hand, there is a number of challenges that need to be resolved before it can be…

In order to accelerate molecular dynamics simulations, it is very common to impose holonomic constraints on their hardest degrees of freedom. In this way, the time step used to integrate the equations of motion can be increased, thus…

All-electron calculations play an important role in density functional theory, in which improving computational efficiency is one of the most needed and challenging tasks. In the model formulations, both nonlinear eigenvalue problem and…

We propose a framework using normalizing-flow based models, SELF-Referencing Embedded Strings, and multi-objective optimization that efficiently generates small molecules. With an initial training set of only 100 small molecules, FastFlows…