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The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute…

Virtual screening of large compound libraries to identify potential hit candidates is one of the earliest steps in drug discovery. As the size of commercially available compound collections grows exponentially to the scale of billions,…

In this paper, we investigate the scheduling design of a mobile edge computing (MEC) system, where active mobile devices with computation tasks randomly appear in a cell. Every task can be computed at either the mobile device or the MEC…

Information on protein-protein interactions (PPIs) not only advances our understanding of molecular biology but also provides important clues for target selection in drug discovery and the design of PPI inhibitors. One of the techniques…

The partitioning of small molecules in cell membranes---a key parameter for pharmaceutical applications---typically relies on experimentally-available bulk partitioning coefficients. Computer simulations provide a structural resolution of…

Many researches have been working on the protein folding problem from more than half century. Protein folding is indeed one of the major unsolved problems in science. In this work, we discuss a model for the simulation of protein…

We consider the problem of controlling a fully specified Markov decision process (MDP), also known as the planning problem, when the state space is very large and calculating the optimal policy is intractable. Instead, we pursue the more…

Direct Preference Optimization (DPO) is an effective approach for aligning protein language models with experimental design goals. However, DPO faces a scalability bottleneck: the number of possible training pairs grows quadratically with…

To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…

The main challenge in controlling hybrid systems arises from having to consider an exponential number of sequences of future modes to make good long-term decisions. Model predictive control (MPC) computes a control action through a…

Modular reconfigurable manipulators enable quick adaptation and versatility to address different application environments and tailor to the specific requirements of the tasks. Task performance significantly depends on the manipulator's…

Robots often face challenges in domestic environments where visual feedback is ineffective, such as retrieving objects obstructed by occlusions or finding a light switch in the dark. In these cases, utilizing contacts to localize the target…

The simulated self-assembly of molecular building blocks into functional complexes is a key area of study in computational biology and materials science. Self-assembly simulations of proteins using physically-motivated potentials for…

In this work we investigate the min-max-min robust optimization problem and the k-adaptability robust optimization problem for binary problems with uncertain costs. The idea of the first approach is to calculate a set of k feasible…

We consider the problem of approximating the reachability probabilities in Markov decision processes (MDP) with uncountable (continuous) state and action spaces. While there are algorithms that, for special classes of such MDP, provide a…

Reachability computations that rely on learned or estimated models require calibration in order to uphold confidence about their guarantees. Calibration generally involves sampling scenarios inside the reachable set. However, producing…

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…

-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…

With the mounting global interest for optical see-through head-mounted displays (OST-HMDs) across medical, industrial and entertainment settings, many systems with different capabilities are rapidly entering the market. Despite such…

State-of-the-art approaches to footstep planning assume reduced-order dynamics when solving the combinatorial problem of selecting contact surfaces in real time. However, in exchange for computational efficiency, these approaches ignore…