Related papers: Rapid sampling of all-atom peptides using a librar…

Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging…

Accurately predicting protein-ligand binding free energies (BFEs) remains a central challenge in drug discovery, particularly because the most reliable methods, such as free energy perturbation (FEP), are computationally intensive and…

Ensemble calculations are essential for systems with uncertain data but require substantial increase in computational resources. This increase severely limits ensemble size. To reach beyond current limits, we present a first-order…

We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by…

We propose an exact slice sampler for Hierarchical Dirichlet process (HDP) and its associated mixture models (Teh et al., 2006). Although there are existing MCMC algorithms for sampling from the HDP, a slice sampler has been missing from…

We propose efficient techniques for generating independent identically distributed uniform random samples inside semialgebraic sets. The proposed algorithm leverages recent results on the approximation of indicator functions by polynomials…

Anticancer peptides (ACPs) are a group of peptides that exhibite antineoplastic properties. The utilization of ACPs in cancer prevention can present a viable substitute for conventional cancer therapeutics, as they possess a higher degree…

We introduce FragFM, a novel hierarchical framework via fragment-level discrete flow matching for efficient molecular graph generation. FragFM generates molecules at the fragment level, leveraging a coarse-to-fine autoencoder to reconstruct…

Sampling equilibrium ensembles of dense polymer mixtures is a paradigmatically hard problem in computational physics, even in lattice-based models. Here, we develop a formalism based on interacting binary tensors that allows for tackling…

We present a Quality by Design (QbD) styled approach for optimizing lipid nanoparticle (LNP) formulations, aiming to offer scientists an accessible workflow. The inherent restriction in these studies, where the molar ratios of ionizable,…

We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…

Sampling from a categorical distribution is mathematically simple, but in large-vocabulary decoding, it often triggers extra memory traffic and extra kernels after the LM head. We present FlashSampling, an exact sampling primitive that…

Interpolation is a fundamental technique in scientific computing and is at the heart of many scientific visualization techniques. There is usually a trade-off between the approximation capabilities of an interpolation scheme and its…

We demonstrate that the recently proposed pruned-enriched Rosenbluth method (P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient algorithms for the folding of simple model proteins. We test them on several models for…

Searching for novel molecular compounds with desired properties is an important problem in drug discovery. Many existing frameworks generate molecules one atom at a time. We instead propose a flexible editing paradigm that generates…

A new molecular simulation toolkit composed of some lately developed force fields and specified models is presented to study the self-assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by utilizing the…

Fast algorithms for the computation of $N$-body problems can be broadly classified into mesh-based interpolation methods, and hierarchical or multiresolution methods. To this last class belongs the well-known fast multipole method (FMM),…

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…

In biochemistry, heteropolymers encoding biological information are assembled out of equilibrium by sequentially incorporating available monomers found in the environment. Current models of polymerization treat monomer incorporation as a…

Fragment-Based Drug Discovery (FBDD) is a popular approach in early drug development, but designing effective linkers to combine disconnected molecular fragments into chemically and pharmacologically viable candidates remains challenging.…