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Network inference has been attracting increasing attention in several fields, notably systems biology, control engineering and biomedicine. To develop a therapy, it is essential to understand the connectivity of biochemical units and the…

Systems and Control · Electrical Eng. & Systems 2024-12-20 Junyang Jin , Ye Yuan , Jorge Goncalves

A microscopic understanding of low-temperature thermodynamics and its relation to dynamical features such as a fragile-to-strong crossover (FSC) remains a central challenge in glass physics. Using swap Monte Carlo combined with a full…

Soft Condensed Matter · Physics 2026-05-25 Anshul D. S. Parmar , Simon G. Kellers , Andreas Heuer

The free energy landscape of the Sherrington-Kirkpatrik (SK) Ising spin glass is simple in the framework of the Thouless-Anderson-Palmer (TAP) equations as each solution (which are minima of the free energy) has associated with it a nearby…

Disordered Systems and Neural Networks · Physics 2022-03-29 T. Aspelmeier , M. A. Moore

The maximum-weight matching problem and the behavior of its energy landscape is numerically investigated. We apply a perturbation method adapted from the analysis of spin glasses. This gives inside into the complexity of the energy…

Disordered Systems and Neural Networks · Physics 2023-04-04 Till Kahlke , Alexander K. Hartmann

We present an efficient algorithm for calculating the minimum energy path (MEP) and energy barriers between local minima on a multidimensional potential energy surface (PES). Such paths play a central role in the understanding of transition…

Computational Physics · Physics 2012-04-19 Amit Samanta , Weinan E

The `lid' algorithm performs an exhaustive exploration of neighborhoods of local energy minima of energy landscapes. This paper describes an implementation of the algorithm, including issues of parallel performance and scalability. To…

Computational Physics · Physics 2009-10-31 Paolo Sibani , Ruud van der Pas , J. Christian Schoen

The equilibrium state of a superfluid in a rotating cylindrical vessel is a vortex crystal -- an array of vortex lines which is stationary in the rotating frame. Experimental realisations of this behaviour typically show a sequence of…

Fluid Dynamics · Physics 2023-10-31 Andrew Cleary , Jacob Page

Kinetic traps are a notorious problem in equilibrium statistical mechanics, where temperature quenches ultimately fail to bring the system to low energy configurations. Using multifarious self-assembly as a model system, we introduce a…

Statistical Mechanics · Physics 2024-07-15 Saeed Osat , Jakob Metson , Mehran Kardar , Ramin Golestanian

Multi-goal robot manipulation tasks with sparse rewards are difficult for reinforcement learning (RL) algorithms due to the inefficiency in collecting successful experiences. Recent algorithms such as Hindsight Experience Replay (HER)…

Robotics · Computer Science 2024-02-26 Erdi Sayar , Zhenshan Bing , Carlo D'Eramo , Ozgur S. Oguz , Alois Knoll

Strongly coupled immersed boundary (IB) methods solve the nonlinear fluid and structural equations of motion simultaneously for strongly enforcing the no-slip constraint on the body. Handling this constraint requires solving several large…

Fluid Dynamics · Physics 2021-03-12 Nirmal Jayaprasad Nair , Andres Goza

This paper studies the inverse problem related to the identification of the flexural stiffness of an Euler Bernoulli beam in order to reconstruct its profile starting from available response data. The proposed identification procedure makes…

Computational Engineering, Finance, and Science · Computer Science 2019-07-09 A. Greco , A. Pluchino , S. Caddemi , I. Caliò , F. Cannizzaro

This paper proposes energy-efficient coordinated beamforming strategies for multi-cell multi-user multiple-input single-output system. We consider a practical power consumption model, where part of the consumed power depends on the base…

Information Theory · Computer Science 2017-10-03 Oskari Tervo , Antti Tölli , Markku Juntti , Le-Nam Tran

By performing a stochastic dynamic in a space of Slater determinants, the Full Configuration Interaction Quantum Monte Carlo (FCIQMC) method has been able to obtain energies which are essentially free from systematic error to the basis set…

Computational Physics · Physics 2014-10-10 George H. Booth , Deidre Cleland , Ali Alavi , David P. Tew

Popular methods for identifying transition paths between energy minima, such as the nudged elastic band and string methods, typically do not incorporate potential energy curvature information, leading to slow relaxation to the minimum…

Computational Physics · Physics 2019-03-11 Stela Makri , Christoph Ortner , James R. Kermode

In this article we introduce a multi-modal variational method to analytically estimate the full number- and corresponding energy-density profile of a spin-1 Bose-Einstein condensate (BEC) for a number of particles as low as 500 under…

Quantum Gases · Physics 2023-01-18 Projjwal K. Kanjilal , A. Bhattacharyay

It is analyzed whether the potential energy landscape of a glass-forming system can be effectively mapped on a random model which is described in statistical terms. For this purpose we generalize the simple trap model of Bouchaud and…

Disordered Systems and Neural Networks · Physics 2009-11-11 A. Heuer , B. Doliwa , A. Saksaengwijit

A first-principles based methodology for efficiently and accurately finding thermodynamically stable and metastable atomic structures is introduced and benchmarked. The approach is demonstrated for gas-phase metal-oxide clusters in…

We describe a new technique for computing lower-bounds on the minimum energy configuration of a planar Markov Random Field (MRF). Our method successively adds large numbers of constraints and enforces consistency over binary projections of…

Machine Learning · Computer Science 2012-02-20 Julian Yarkony , Ragib Morshed , Alexander T. Ihler , Charless C. Fowlkes

Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…

Disordered Systems and Neural Networks · Physics 2009-10-30 Shoji Takada , Peter G. Wolynes

We introduce a `virtual-move' Monte Carlo (VMMC) algorithm for systems of pairwise-interacting particles. This algorithm facilitates the simulation of particles possessing attractions of short range and arbitrary strength and geometry, an…

Statistical Mechanics · Physics 2009-11-11 Stephen Whitelam , Phillip L. Geissler