Related papers: Approximating Free Energy and Committor Landscapes…
The paper proposes a method for measuring available bandwidth, based on testing network packets of various sizes (Variable Packet Size method, VPS). The boundaries of applicability of the model have been found, which are based on the…
Next-generation datacenters require highly efficient network load balancing to manage the growing scale of artificial intelligence (AI) training and general datacenter traffic. However, existing Ethernet-based solutions, such as Equal Cost…
The kinetics of collective rearrangements in solution, such as protein folding and nanocrystal phase transitions, often involve free energy barriers that are both long and rough. Applying methods of transition path sampling to harvest…
Free energy landscapes encode the kinetics, intermediates, and transition states that govern molecular processes and are thus a key target of single biomolecule research. Typical approaches to deriving optimal, error-minimizing,…
One of the key limitations of Molecular Dynamics simulations is the computational intractability of sampling protein conformational landscapes associated with either large system size or long timescales. To overcome this bottleneck, we…
A new particle-based sampling and approximate inference method, based on electrostatics and Newton mechanics principles, is introduced with theoretical ground, algorithm design and experimental validation. This method simulates an…
We present a new and efficient method for computing the transition pathways, free energy barriers, and transition rates in complex systems with relatively smooth energy landscapes. The method proceeds by evolving strings, i.e. smooth curves…
The use of random sampling in decision-making and control has become popular with the ease of access to graphic processing units that can generate and calculate multiple random trajectories for real-time robotic applications. In contrast to…
The study by Jung et al. (Jung H, Covino R, Arjun A, et al., Nat Comput Sci. 3:334-345 (2023)) introduced Artificial Intelligence for Molecular Mechanism Discovery (AIMMD), a novel sampling algorithm that integrates machine learning to…
Rare events such as nucleation processes are of ubiquitous importance in real systems. The most popular method for nonequilibrium systems, forward flux sampling (FFS), samples rare events by using interfaces to partition the whole…
Wireless sensing and wireless energy are enablers to pave the way for smart transportation and a greener future. In this paper, an intelligent reflecting surface (IRS) assisted integrated sensing and wireless power transfer (ISWPT) system…
We present Path Integral Sampler~(PIS), a novel algorithm to draw samples from unnormalized probability density functions. The PIS is built on the Schr\"odinger bridge problem which aims to recover the most likely evolution of a diffusion…
The modern theory of rare events is grounded in near equilibrium ideas, however many systems of modern interest are sufficiently far from equilibrium that traditional approaches do not apply. Using the recently developed variational path…
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…
Tensors with finite correlation afford very compact tensor network representations. A novel tensor network-based decomposition of real-time path integral simulations involving Feynman-Vernon influence functional is introduced. In this…
We apply the "weighted ensemble" (WE) simulation strategy, previously employed in the context of molecular dynamics simulations, to a series of systems-biology models that range in complexity from one-dimensional to a system with 354…
The primary limitation for the application of alchemical free energy methods to a wider variety of complex molecular systems is achieving reasonable sampling. Flexible binding complexes often have high free energy barriers, which require…
Predicting and characterizing phase transitions is crucial for understanding generic physical phenomena such as crystallization, protein folding and others. However, directly observing phase transitions is not always easy, and often one has…
Introduction. Treatment planning systems (TPS) are an essential component for simulating and optimizing a radiation therapy treatment before administering it to the patient. It ensures that the tumor is well covered and the dose to the…
In adaptive-bias enhanced sampling methods, a bias potential is added to the system to drive transitions between metastable states. The bias potential is a function of a few collective variables and is gradually modified according to the…