相关论文: Metabolic Flux Analysis in Isotope Labeling Experi…
This article presents a modeling framework for a class of multiphase chemical systems based on non-equilibrium thermodynamics. Compartmental modeling is used to establish the dynamic properties of liquid-vapor systems operating far from…
Nonadiabatic molecular dynamics is a key technique for investigating a broad range of photochemical and photophysical processes. Among the established approaches, surface hopping schemes are widely used and can be easily integrated with…
In this paper, we study the least-squares finite element methods (LSFEM) for the linear hyperbolic transport equations. The linear transport equation naturally allows discontinuous solutions and discontinuous inflow conditions, while the…
We present an efficient sampling method for computing a partition function and accelerating configuration sampling. The method performs a random walk in the $\lambda$ space, with $\lambda$ being any thermodynamic variable that characterizes…
In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact uniform sampling of the steady state fluxes in a genome…
Integrative modeling of macromolecular assemblies allows for structural characterization of large assemblies that are recalcitrant to direct experimental observation. A Bayesian inference approach facilitates combining data from…
In this article we consider an optimization problem where the objective function is evaluated at the fixed-point of a contraction mapping parameterized by a control variable, and optimization takes place over this control variable. Since…
Motivated by the pressing challenges in the digital twin development for biomanufacturing systems, we introduce an adjoint sensitivity analysis (SA) approach to expedite the learning of mechanistic model parameters. In this paper, we…
The control and manipulation of quantum systems without excitation is challenging, due to the complexities in fully modeling such systems accurately and the difficulties in controlling these inherently fragile systems experimentally. For…
Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range…
We study the electrophoretic separation of polyelectrolytes of varying lengths by means of end-labeled free-solution electrophoresis (ELFSE). A coarse-grained molecular dynamics simulation model, using full electrostatic interactions and a…
Microorganisms have developed complex regulatory features controlling their reaction and internal adaptation to changing environments. When modeling these organisms we usually do not have full understanding of the regulation and rely on…
Currently existing energy-stable parametric finite element methods for surface diffusion flow and other flows are usually limited to first-order accuracy in time. Designing a high-order algorithm for geometric flows that can also be…
In the flow and transport numerical simulation, mesh adaptivity strategy is important in reducing the usage of CPU time and memory. The refinement based on the pressure error estimator is commonly-used approach without considering the flux…
This study presents an efficient algebraic scheme known as MULES for sharp interface advection, verified against various schemes including first-order upwind, second-order central, van Leer flux limiter, and Geometric Volume-of-Fluid (VOF).…
In response to the growing need for generating real-world evidence from multi-site collaborative studies, we introduce an efficient collaborative learning approach to evaluate average treatment effect (ECO-ATE) in a multi-site setting under…
Cells adapt their metabolic fluxes in response to changes in the environment. We present a framework for the systematic construction of flux-based graphs derived from organism-wide metabolic networks. Our graphs encode the directionality of…
In one calculation, adjoint sensitivity analysis provides the gradient of a quantity of interest with respect to all system's parameters. Conventionally, adjoint solvers need to be implemented by differentiating computational models, which…
This paper introduces a novel method for numerically stabilizing sequential continuous adjoint flow solvers utilizing an elliptic relaxation strategy. The proposed approach is formulated as a Partial Differential Equation (PDE) containing a…
We introduce a new path integral Monte Carlo method for investigating nonadiabatic systems in thermal equilibrium and demonstrate an approach to reducing stochastic error. We derive a general path integral expression for the partition…