Related papers: Improving sampling of binding free energy differen…
Fragmentation methods such as the many-body expansion (MBE) are a common strategy to model large systems by partitioning energies into a hierarchy of decreasingly significant contributions. The number of fragments required for chemical…
Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure.…
Fast and accurate large-scale energy system models are needed to investigate the potential of storage to complement the fluctuating energy production of renewable energy systems. However, standard Mixed-Integer Programming (MIP) models that…
The many-body expansion (MBE) is an efficient tool which has a long history of use for calculating interaction energies, binding energies, lattice energies, and so on. In the past, applications of MBE to correlation energy have been…
Macromolecular and biomolecular folding landscapes typically contain high free energy barriers that impede efficient sampling of configurational space by standard molecular dynamics simulation. Biased sampling can artificially drive the…
Recent masked diffusion models (MDMs) have shown competitive performance compared to autoregressive models (ARMs) for language modeling. While most literature has focused on performance enhancing sampling procedures, efficient sampling from…
Bayesian inference for factorial hidden Markov models is challenging due to the exponentially sized latent variable space. Standard Monte Carlo samplers can have difficulties effectively exploring the posterior landscape and are often…
We consider the problem of sampling transition paths between two given metastable states of a molecular system, e.g. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…
The key issue in importance sampling is the choice of the alternative sampling distribution, which is often chosen from the exponential tilt family of the underlying distribution. However, when the problem exhibits certain kind of…
We investigate the mechanism of chain exchange in diblock copolymer micelles using two distinct yet complementary simulation techniques. First, enhanced sampling method is combined with coarse-grained molecular dynamics to compute a…
The spectral and energy efficiency (SE-EE) trade-off in pinching-antenna systems (PASS) is investigated in this paper. In particular, two practical operating protocols, namely waveguide multiplexing (WM) and waveguide switching (WS), are…
Enhanced sampling methods such as metadynamics and umbrella sampling have become essential tools for exploring the configuration space of molecules and materials. At the same time, they have long faced a number of issues such as the…
Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can…
Extracting associations that recur across multiple studies while controlling the false discovery rate is a fundamental challenge. Here, we consider an extension of Efron's single-study two-groups model to allow joint analysis of multiple…
This thesis includes analysis of disordered spin ensembles corresponding to Exact Cover, a multi-access channel problem, and composite models combining sparse and dense interactions. The satisfiability problem in Exact Cover is addressed…
An Automated Sliced Gibbs framework is proposed for fully automated Markov chain Monte Carlo sampling from arbitrary finite dimensional probability kernels. The method targets unnormalized, non-smooth, heavy tailed, and highly multimodal…
This paper investigates a rotatable antenna (RA) assisted mobile edge computing (MEC) network, where multiple users offload their computation tasks to an edge server equipped with an RA array under a time-division multiple access protocol.…
Umbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when multiple parallel channels along the reaction coordinate or hidden barriers in directions…
Because of their multimodality, mixture posterior distributions are difficult to sample with standard Markov chain Monte Carlo (MCMC) methods. We propose a strategy to enhance the sampling of MCMC in this context, using a biasing procedure…