Related papers: Constraint methods for determining pathways and fr…
Chemical reactions are commonly described by the reactive flux transferring population from reactants to products across a double-well free energy barrier. Dynamics often involves barrier recrossing and quantum effects like tunneling,…
In order to satisfy safety conditions, an agent may be constrained from acting freely. A safe controller can be designed a priori if an environment is well understood, but not when learning is employed. In particular, reinforcement learned…
Granular materials such as sand, powders, and food grains are ubiquitous in civil engineering, geoscience, agriculture, and medicine. While the influence of friction between the grains on the static structure of these systems is well…
We propose an efficient method to compute reaction rate constants of thermally activated processes occurring in many-body systems at finite temperature. The method consists in two steps: first, paths are sampled using a transition path…
Learning from Demonstration allows robots to mimic human actions. However, these methods do not model constraints crucial to ensure safety of the learned skill. Moreover, even when explicitly modelling constraints, they rely on the…
The predictive ability of stochastic chemical reactions is currently limited by the lack of closed form solutions to the governing chemical master equation. To overcome this limitation, this paper proposes a computational method capable of…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
Transition path sampling is a method for estimating the rates of rare events in molecular systems based on the gradual transformation of a path distribution containing a small fraction of reactive trajectories into a biased distribution in…
In order to increase the efficiency of the computer simulation of biological molecules, it is very common to impose holonomic constraints on the fastest degrees of freedom; normally bond lengths, but also possibly bond angles. However, as…
The computation of free energy differences through an exponential weighting of out of equilibrium paths (known as the Jarzynski equality) is often used for transitions between states described by an external parameter $\lambda$ in the…
A recently developed model chemistry (jun-Cheap) has been slightly modified and proposed as an effective, reliable and parameter-free scheme for the computation of accurate reaction rates with special reference to astrochemical and…
Control barrier functions (CBF) are widely explored to enforce the safety-critical constraints on nonlinear systems recently. There are many researchers incorporating the control barrier functions into path planning algorithms to find a…
The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result,…
When deploying autonomous agents in unstructured environments over sustained periods of time, adaptability and robustness oftentimes outweigh optimality as a primary consideration. In other words, safety and survivability constraints play a…
The unconstrained ensemble describes completely open systems whose control parameters are chemical potential, pressure, and temperature. For macroscopic systems with short-range interactions, thermodynamics prevents the simultaneous use of…
Understanding pedestrian behavior is crucial for the safe deployment of Autonomous Vehicles (AVs) in urban environments. Traditional pedestrian behavior models often fall into two categories: mechanistic models, which do not generalize well…
Using molecular simulation, we study the nucleation of liquid droplets from binary mixtures and determine the free energy of nucleation along entropic pathways. To this aim, we develop the $\mu_1 \mu_2 VT-S$ method, based on the…
Stable dynamical systems are a flexible tool to plan robotic motions in real-time. In the robotic literature, dynamical system motions are typically planned without considering possible limitations in the robot's workspace. This work…
We define and study a class of (random) Boolean constraint satisfaction problems representing minimal feasibility constraints for networks of chemical reactions. The constraints we consider encode, respectively, for hard mass-balance…
Predicting crystal nucleation is among the most significant long--standing challenges in condensed matter. In the system most studied (hard sphere colloids), the comparison between experiments performed using static light scattering and…