Related papers: Improved fragment-based movement with LRFragLib fo…
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…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
Protein inverse folding aims to identify viable amino acid sequences that can fold into given protein structures, enabling the design of novel proteins with desired functions for applications in drug discovery, enzyme engineering, and…
Pre-calculated libraries of molecular fragment configurations have previously been used as a basis for both equilibrium sampling (via "library-based Monte Carlo") and for obtaining absolute free energies using a polymer-growth formalism.…
We present Light3R-SfM, a feed-forward, end-to-end learnable framework for efficient large-scale Structure-from-Motion (SfM) from unconstrained image collections. Unlike existing SfM solutions that rely on costly matching and global…
Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were…
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…
We demonstrate that the recently proposed pruned-enriched Rosenbluth method PERM (P.~Grassberger, Phys.~Rev.~{\bf E 56} (1997) 3682) leads to very efficient algorithms for the folding of simple model proteins. We test it on several models…
We present a model-based framework for robot locomotion that achieves walking based on only 4.5 minutes (45,000 control steps) of data collected on a quadruped robot. To accurately model the robot's dynamics over a long horizon, we…
Robust estimation is essential in computer vision, robotics, and navigation, aiming to minimize the impact of outlier measurements for improved accuracy. We present a fast algorithm for Geman-McClure robust estimation, FracGM, leveraging…
Ensuring software quality remains a critical challenge in complex and dynamic development environments, where software defects can result in significant operational and financial risks. This paper proposes an innovative framework for…
Energy evaluation using fast Fourier transforms enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods efficient acceleration is achieved only in either…
Legged robots, specifically quadrupeds, are becoming increasingly attractive for industrial applications such as inspection. However, to leave the laboratory and to become useful to an end user requires reliability in harsh conditions. From…
In this work, we introduce a control framework that combines model-based footstep planning with Reinforcement Learning (RL), leveraging desired footstep patterns derived from the Linear Inverted Pendulum (LIP) dynamics. Utilizing the LIP…
A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The…
The remarkable structural diversity of modern proteins reflects millions of years of evolution, during which sequence space has expanded while many structural features remain conserved. This conservation is evident not only among homologous…
This work presents an efficient framework to generate a motion plan of a robot with high degrees of freedom (e.g., a humanoid robot). High-dimensionality of the robot configuration space often leads to difficulties in utilizing the…
In robots task and motion planning (TAMP), it is crucial to sample within the robot's configuration space to meet task-level global constraints and enhance the efficiency of subsequent motion planning. Due to the complexity of joint…
A novel approach is presented for computing flexible body dynamics based on conventional structural dynamics models. This approach innovatively captures the rigid body motion component embedded within a flexible body's movement, generates…
The current work on reinforcement learning (RL) from demonstrations often assumes the demonstrations are samples from an optimal policy, an unrealistic assumption in practice. When demonstrations are generated by sub-optimal policies or…