1,721,009 research outputs found
A Short Introduction to the Molecular Dynamics Simulation of Nanomaterials
No full textIn the last 25 years, computational chemistry has become a fundamental research methodology in all areas of nanoscience. Computer simulations are powerful nano- scopes that can reveal details of molecular processes on lengths of space and time inaccessible to experimental observations. Along with clarifying the physicochemical properties of single molecules or systems, they provide insights for helping the design and manufacturing of new nanomaterials and nanodevices. Among the various computational methods, Molecular Dynamics (MD) simulation is a powerful approach to analyzing structural and dynamic properties of nanomaterials at different time and space scales. This chapter aims to provide a general and concise introduction to the MD simulations of molecular systems by showing some examples of applications for studying biological macromolecules and nanomaterials.</p
A short introduction to the molecular dynamics simulation of nanomaterials
No full textIn the last 20 years, computational chemistry has become a very important research methodology in all areas of nanoscience. Computer simulations are powerful nano-scopes that can to reveal details of molecular processes on lengths of space and time unreachable to experimental observations. Along clarifying the physicochemical properties of single molecules or systems, they provide insights for helping designing and manufacturing of new nanomaterials and nanodevices. Among the various computational methods, Molecular Dynamics simulation is a powerful approach to analyze both structural and dynamic properties ones at a different scale of time and space. This chapter aims to provide a general and concise introduction to the MD simulations of molecular systems by showing some example of applications to the study of biological macromolecules and nanomaterials.</p
Quantitative Integration of FRET and Molecular Dynamics for Modeling Flexible Peptides
No full textFlexible protein regions, often enriched in glycine- and serine-rich segments, play a central role in biomolecular dynamics and function. The combination of time-resolved fluorescence resonance energy transfer (FRET) spectroscopy and molecular dynamics simulations provides a powerful framework to characterize these motions at atomic resolution. In this work, we investigate the conformational and kinetic properties of Trp-(GS)n-Dbo and Trp-(PP)n-Dbo peptides (n = 0,1,2,3) in aqueous solution using microsecond-scale MD simulations, informed by an improved description of the Dbo-labeled aspartic residue compatible with the G54A7 force field. The simulations quantitatively reproduce experimental end-to-end distances derived from FRET measurements, with deviations below 5% for all (GS)n peptides, and correctly capture the systematic relationship between chain flexibility and fluorophore separation. Analysis of looping kinetics further shows quantitative agreement with experimentally measured contact formation rates after viscosity correction, supporting a diffusion-controlled mechanism for intrachain contact formation. Together, these results establish a consistent, quantitative link between structural ensembles, dynamical observables, and FRET experiments, and provide benchmark data for modeling fluorophore-labeled peptides and intrinsically disordered protein segments.</p
Principal Component Analysis of Molecular Dynamics Trajectories: Concepts, Tools, and Applications
No full textPrincipal component analysis (PCA) is a central tool for extracting essential information from complex datasets and has become widely used in the study of dynamical systems across disciplines. Its interdisciplinary relevance spans physics, chemistry, biology, computer science, and applied mathematics, where PCA and related approaches serve as gateways to understanding structure–function relationships, emergent behavior, and data- driven modeling. In the theoretical study of biomolecular systems using molecular dynamics (MD) simulations method, PCA filters high- dimensional trajectories into a reduced set of collective motions that elucidate conformational transitions and functional mechanisms. PCA provides an intuitive framework to connect statistical variance with dominant dynamical modes, a concept that extends naturally to the atomic scale of biomolecules. Modern developments integrate PCA with time- lagged methods, Markov state models, nonlinear dimensionality reduction, and machine learning techniques. These advances capture slow modes, rare events, and nonlinear manifolds, enriching the understanding of MD simulations results. A variety of computational packages now provide PCA- based analyses, supporting workflows from raw trajectory processing to visualization of free- energy landscapes and structural conformations. Applications range from probing peptide folding and protein domain motions to exploring collective dynamics in large assemblies. Since their first application more than 30 years ago to MD simulation, PCA- based methods continue to enhance the ability to analyze complex dynamical systems, offering a unifying statistical perspective that connects molecular simulations with interdisciplinary approaches to high- dimensional data analysis.</p
Structure, dynamics, and function of the monooxygenase P450 BM-3: insights from computer simulations studies
No full textThe monooxygenase P450 BM-3 is a NADPH-dependent fatty acid hydroxylase enzyme isolated from soil bacterium Bacillus megaterium. As a pivotal member of cytochrome P450 superfamily, it has been intensely studied for the comprehension of structure-dynamics-function relationships in this class of enzymes. In addition, due to its peculiar properties, it is also a promising enzyme for biochemical and biomedical applications. However, despite the efforts, the full understanding of the enzyme structure and dynamics is not yet achieved. Computational studies, particularly molecular dynamics (MD) simulations, have importantly contributed to this endeavor by providing new insights at an atomic level regarding the correlations between structure, dynamics, and function of the protein. This topical review summarizes computational studies based on MD simulations of the cytochrome P450 BM-3 and gives an outlook on future directions.</p
A Short Introduction to the Molecular Dynamics Simulation of Nanomaterials
No full textIn the last 25 years, computational chemistry has become a fundamental research methodology in all areas of nanoscience. Computer simulations are powerful nano- scopes that can reveal details of molecular processes on lengths of space and time inaccessible to experimental observations. Along with clarifying the physicochemical properties of single molecules or systems, they provide insights for helping the design and manufacturing of new nanomaterials and nanodevices. Among the various computational methods, Molecular Dynamics (MD) simulation is a powerful approach to analyzing structural and dynamic properties of nanomaterials at different time and space scales. This chapter aims to provide a general and concise introduction to the MD simulations of molecular systems by showing some examples of applications for studying biological macromolecules and nanomaterials.</p
A Molecular Dynamics Simulation Study of Glycine/Serine Octa Peptides Labeled with 2,3-diazabicyclo [2.2.2] oct-2-ene Fluorophore
No full textThe 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) is a versatile fluorophore widely used in F\"orster resonance energy transfer (FRET) spectroscopy studies due to its remarkable sensitivity, enabling precise donor-acceptor distance measurements, even for short peptides. Integrating time-resolved and FRET spectroscopy with molecular dynamics simulations provides a robust approach to unravel the structure and dynamics of biopolymers in solution. This study investigates the structural behavior of three octapeptide variants: Trp-(Gly-Ser)-Dbo, Trp-(GlyGly)-Dbo, and Trp-(SerSer)-Dbo, where Dbo represents the DBO-containing modified aspartic acid, using molecular dynamics simulations. Glycine and serine-rich amino acid fragments, common in flexible protein regions, play essential roles in functional properties.
Results show excellent agreement between end-to-end distances, orientational factors from simulations, and available experimental and theoretical data, validating the reliability of the GROMOS force field model. The end-to-end distribution, modeled using three Gaussian distributions, reveals a complex shape, confirmed by cluster analysis highlighting a limited number of significant conformations dominating the peptide landscape. All peptides predominantly adopt a disordered state in the solvent, yet exhibit a compact shape, aligning with the model of disordered polypeptide chains in poor solvents. Conformations show marginal dependence on chain composition, with Ser-only chains exhibiting slightly more elongation. This study enhances our understanding of peptide behavior, providing valuable insights into their structural dynamics in solution.</p
A short introduction to the molecular dynamics simulation of nanomaterials
No full textIn the last 20 years, computational chemistry has become a very important research methodology in all areas of nanoscience. Computer simulations are powerful nano-scopes that can to reveal details of molecular processes on lengths of space and time unreachable to experimental observations. Along clarifying the physicochemical properties of single molecules or systems, they provide insights for helping designing and manufacturing of new nanomaterials and nanodevices. Among the various computational methods, Molecular Dynamics simulation is a powerful approach to analyze both structural and dynamic properties ones at a different scale of time and space. This chapter aims to provide a general and concise introduction to the MD simulations of molecular systems by showing some example of applications to the study of biological macromolecules and nanomaterials.</p
Structure, dynamics, and function of the monooxygenase P450 BM-3: insights from computer simulations studies
No full textThe monooxygenase P450 BM-3 is a NADPH-dependent fatty acid hydroxylase enzyme isolated from soil bacterium Bacillus megaterium. As a pivotal member of cytochrome P450 superfamily, it has been intensely studied for the comprehension of structure-dynamics-function relationships in this class of enzymes. In addition, due to its peculiar properties, it is also a promising enzyme for biochemical and biomedical applications. However, despite the efforts, the full understanding of the enzyme structure and dynamics is not yet achieved. Computational studies, particularly molecular dynamics (MD) simulations, have importantly contributed to this endeavor by providing new insights at an atomic level regarding the correlations between structure, dynamics, and function of the protein. This topical review summarizes computational studies based on MD simulations of the cytochrome P450 BM-3 and gives an outlook on future directions.</p
The KaleidoPhoneScope: New Tricks For an Old Device
No full textLissajous-Bowditch curves have fascinated scientists, artists, and educators for over a century due to their mesmerizing beauty and versatile applications across various scientific fields. This paper delves into exploring these curves, not only as aesthetic marvels but also as powerful tools for scientific inquiry and educational activities. In particular, we present a practical activity centred around the construction of a modernized version of Wheatstone’s Kalei- dophone, aptly named the KaleidoPhoneScope, using cost-effective and readily available materials. The construction process entails 3D printing components of the device, which are complemented by the integration of a laser module and Raspberry Pi microcomputer for video recording and data analysis facilitated by a Python program. Beyond the immediate focus on Lissajous-Bowditch cur- ves, this paper highlights the potential for extending the device’s use to study other phenomena related to vibrational motion. Utilizing the principles behind the construction of the KaleidoPhoneScope, educators and learners can explore a wide range of vibration-related phenomena, fostering a deeper understanding of fundamental principles in physics and engineering. This paper bridges theore- tical insights with practical application, providing educators and learners with a valuable resource to not only enhance their understanding of Lissajous-Bowditch curves but also to engage in a stimulating educational experience that encourages exploration, experimentation, and innovation.</p
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