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The accurate estimation of free energy differences between two states is a long-standing challenge in molecular simulations. Traditional approaches generally rely on sampling multiple intermediate states to ensure sufficient overlap in…
Computer experiments refer to the study of real systems using complex simulation models. They have been widely used as alternatives to physical experiments. Design and analysis of computer experiments have attracted great attention in past…
Single-molecule F\"orster Resonance Energy Transfer (smFRET) is ideally suited to resolve the dynamics of biomolecules. A significant challenge to date is capturing and quantifying the exchange between multiple conformational states, mainly…
A new approach is presented to obtain candidate structures from atomic pair distribution function (PDF) data in a highly automated way. It fetches, from web-based structural databases, all the structures meeting the experimenter's search…
Computer simulations can aid in understanding how collective materials properties emerge from interactions between simple constituents. Here, we introduce a coarse-grained model that enables simulation of networks of actin filaments, myosin…
Predicting the outcome of jet-milling based on the knowledge of process parameters and starting material properties is a task still far from being accomplished. Given the technical difficulties in measuring thermodynamics, flow properties…
Coupling separately developed codes offers an attractive method for increasing the accuracy and fidelity of the computational models. Examples include the earth sciences and fusion integrated modeling. This paper describes the Framework…
Modelling MEMS involves a variety of software tools that deal with the analysis of complex geometrical structures and the assessment of various interactions among different energy domains and components. Moreover, the MEMS market is growing…
Regularized regression models are well studied and, under appropriate conditions, offer fast and statistically interpretable results. However, large data in many applications are heterogeneous in the sense of harboring distributional…
RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensembles, and can thus estimate minimum free-energy structures and…
Constitutive modeling lies at the core of mechanics, allowing us to map strains onto stresses for a material in a given mechanical setting. Historically, researchers relied on phenomenological modeling where simple mathematical…
The goal of the paper is to automatize the selection of mechanisms which are able to describe a set of measurements. In order to do so first we construct a set of possible mechanism fulfilling chemically reasonable requirements with a given…
Computational modeling of a complex system is limited by the parts of the system with the least information. While detailed models and high-resolution data may be available for parts of a system, abstract relationships are often necessary…
Reduced-order models that accurately abstract high fidelity models and enable faster simulation is vital for real-time, model-based diagnosis applications. In this paper, we outline a novel hybrid modeling approach that combines machine…
In computer experiments, a mathematical model implemented on a computer is used to represent complex physical phenomena. These models, known as computer simulators, enable experimental study of a virtual representation of the complex…
In order to improve the fault diagnosis capability of multivariate statistical methods, this article introduces a fault isolation framework based on structured sparsity modeling. The developed method relies on the reconstruction based…
In most of the cases, the experimental study of Nanotechnology involves high cost for Laboratory set-up and the experimentation processes were also slow. So, one cannot rely on experimental nanotechnology alone. As such, the Computer-Based…
Many applications in mechanical, acoustic, and electronic engineering require estimating complex dynamical models, often represented as additive multi-input multi-output (MIMO) transfer functions with structural constraints. This paper…
Accurate prediction of dynamical response of structural system depends on the correct modeling of that system. However, modeling becomes increasingly challenging when there are many candidate models available to describe the system…
Complete reliance on the fitted model in response surface experiments is risky and relaxing this assumption, whether out of necessity or intentionally, requires an experimenter to account for multiple conflicting objectives. This work…