Extending molecular simulation time scales: Parallel in time integrations for           high-level quantum chemistry and complex force representations

Abstract This paper describes the activities launched at SCK•CEN, intended to explore ethical and other non-technical aspects when dealing with the time scales considered in the high-level waste disposal program. (1) Especially the issues of retrievability and precaution will be focused on philosophically. Many questions will be raised in order to sensitize all stakeholders for the transdisciplinary character of the transgenerational problem at hand.

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Imaging localized neuronal activity at fast time scales through biomechanics

Science Advances ◽

10.1126/sciadv.aav3816 ◽

2019 ◽

Vol 5 (4) ◽

pp. eaav3816 ◽

Cited By ~ 9

Author(s):

Samuel Patz ◽

Daniel Fovargue ◽

Katharina Schregel ◽

Navid Nazari ◽

Miklos Palotai ◽

...

Keyword(s):

Time Scales ◽

Neuronal Activity ◽

High Speed ◽

Fast Time ◽

Regional Patterns ◽

Cortical Input ◽

Brain Biomechanics ◽

Neuronal Processes ◽

High Level

Mapping neuronal activity noninvasively is a key requirement for in vivo human neuroscience. Traditional functional magnetic resonance (MR) imaging, with a temporal response of seconds, cannot measure high-level cognitive processes evolving in tens of milliseconds. To advance neuroscience, imaging of fast neuronal processes is required. Here, we show in vivo imaging of fast neuronal processes at 100-ms time scales by quantifying brain biomechanics noninvasively with MR elastography. We show brain stiffness changes of ~10% in response to repetitive electric stimulation of a mouse hind paw over two orders of frequency from 0.1 to 10 Hz. We demonstrate in mice that regional patterns of stiffness modulation are synchronous with stimulus switching and evolve with frequency. For very fast stimuli (100 ms), mechanical changes are mainly located in the thalamus, the relay location for afferent cortical input. Our results demonstrate a new methodology for noninvasively tracking brain functional activity at high speed.

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The nature of intermolecular interactions in pyridinium–anion–β-hexachlorocyclohexane molecular crystals

Physical Chemistry Chemical Physics ◽

10.1039/c7cp02911j ◽

2017 ◽

Vol 19 (31) ◽

pp. 20691-20698 ◽

Cited By ~ 6

Author(s):

I. G. Grosu ◽

M. I. Rednic ◽

M. Miclăuş ◽

I. Grosu ◽

A. Bende

Keyword(s):

Quantum Chemistry ◽

Ab Initio ◽

Intermolecular Interactions ◽

Molecular Crystal ◽

Molecular Crystals ◽

Pyridinium Cations ◽

High Level

The nature of intermolecular interactions in different molecular crystal configurations formed by pyridinium cations, chloride or bromide anions as well as β-hexachlorocyclohexane (β-HCH) molecules has been investigated using high level ab initio quantum chemistry methods.

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Quantum chemistry in the 21st century (Special topic article)

Pure and Applied Chemistry ◽

10.1351/pac200072081405 ◽

2000 ◽

Vol 72 (8) ◽

pp. 1405-1423 ◽

Cited By ~ 15

Author(s):

Christopher J. Barden ◽

Henry F. Schaefer

Keyword(s):

Quantum Chemistry ◽

Density Functional ◽

Special Topic ◽

Future Research ◽

New Era ◽

Incremental Development ◽

Quantum Chemical Methods ◽

Theoretical Predictions ◽

Ready Availability ◽

High Level

Quantum chemistry is the field in which solutions to the Schrödinger equation are used to predict the properties of molecules and solve chemical problems. This paper considers possible future research directions in light of the discipline's past successes. After decades of incremental development—accompanied by a healthy dose of skepticism from the experimental community—the ready availability of fast computers has ushered in a "golden age" of quantum chemistry. In this new era of acceptance, theoretical predictions often precede experiment in small molecule chemistry, and quantum chemical methods play an ever greater role in biochemical and other larger systems. Quantum chemists increasingly divide their efforts along three fronts: high-level (spectroscopic) accuracy for small molecules, characterized by such techniques as Brueckner methods, r12 formalisms, and multireference calculations; parameterization- or extrapolation-based intermediate-level schemes (such as Gaussian-N theory) for medium molecules; and lower-level (chemical) accuracy for large molecules, characterized by density functional theory and linear scaling techniques. These tools, and quantum chemistry as a whole, are examined here from a historical perspective and with a view toward their future applications.

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Developing a Coarse-Grained Model for Secretion of the Passenger Domain of the Autotransporter ESPP to Reach Realistic Simulation Time Scales

Biophysical Journal ◽

10.1016/j.bpj.2020.11.1310 ◽

2021 ◽

Vol 120 (3) ◽

pp. 190a

Author(s):

Lixinhao Yang ◽

Jinchan Liu ◽

James C. Gumbart

Keyword(s):

Time Scales ◽

Coarse Grained ◽

Passenger Domain ◽

Realistic Simulation ◽

Coarse Grained Model ◽

Simulation Time

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When temporal attention lacks confidence

10.1101/496232 ◽

2018 ◽

Author(s):

Samuel Recht ◽

Pascal Mamassian ◽

Vincent de Gardelle

Keyword(s):

Decision Making ◽

Attentional Blink ◽

Time Scales ◽

Item Selection ◽

Temporal Attention ◽

Confidence Judgments ◽

High Level ◽

Selective Process ◽

Different Time Scales ◽

Selection Of

AbstractAccurate decision-making requires estimating the uncertainty of perceptual events. Temporal attention is known to enhance the selection of a stimulus at a relevant time, but how does this selective process affect a decision’s confidence? Here, we adapted an “Attentional blink” paradigm to investigate the effect of temporal attention on confidence judgments. In a RSVP stream of letters, two targets were cued to induce two successive attentional episodes. We found that the confidence ratings given to an item systematically followed the probability with which this item was reported. This coupling made confidence oblivious to selection delays usually observed when the two targets were separated by long intervals (249ms to 747ms). In particular, during this period, confidence was higher for more delayed item selection. One exception to this relationship between confidence and temporal selection was found when the second target appeared soon after (83ms) the first attentional episode. Here, a strong under-confidence bias was observed. Importantly, however, this early confidence bias did not impact confidence sensitivity in discriminating correct and erroneous responses. These results suggest that temporal attention and confidence can operate at different time scales, a difference which seems to reflect high-level heuristic biases rather than segregated processes for decision and confidence evidence.

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Multi Objective PSO with Passive Congregation for Load Balancing Problem

International Journal of Computers Communications & Control ◽

10.15837/ijccc.2021.5.4274 ◽

2021 ◽

Vol 16 (5) ◽

Author(s):

Mohammad Marufuzzaman ◽

Muneed Anjum Timu ◽

Jubayer Sarkar ◽

Aminul Islam ◽

Labonnah Farzana Rahman ◽

...

Keyword(s):

Load Balancing ◽

Interactive Simulation ◽

High Level Architecture ◽

Multi Objective ◽

Distributed Interactive Simulation ◽

High Level ◽

Simulation Time ◽

Pc Method ◽

Better Than ◽

Passive Congregation

High-level architecture (HLA) and Distributed Interactive Simulation (DIS) are commonly used for the distributed system. However, HLA suffers from a resource allocation problem and to solve this issue, optimization of load balancing is required. Efficient load balancing can minimize the simulation time of HLA and this optimization can be done using the multi-objective evolutionary algorithms (MOEA). Multi-Objective Particle Swarm Optimization (MOPSO) based on crowding distance (CD) is a popular MOEA method used to balance HLA load. In this research, the efficiency of MOPSO-CD is further improved by introducing the passive congregation (PC) method. Several simulation tests are done on this improved MOPSO-CD-PC method and the results showed that in terms of Coverage, Spacing, Non-dominated solutions and Inverted generational distance metrics, the MOPSO-CD-PC performed better than the previous MOPSO-CD algorithm. Hence, it can be a useful tool to optimize the load balancing problem in HLA.

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Reducing molecular simulation time for AFM images based on super-resolution methods

Beilstein Journal of Nanotechnology ◽

10.3762/bjnano.12.61 ◽

2021 ◽

Vol 12 ◽

pp. 775-785

Author(s):

Zhipeng Dou ◽

Jianqiang Qian ◽

Yingzi Li ◽

Rui Lin ◽

Jianhai Wang ◽

...

Keyword(s):

Machine Learning ◽

Molecular Simulation ◽

Super Resolution ◽

Training Data ◽

Reconstruction Algorithms ◽

Force Microscopy ◽

Nanoscale Imaging ◽

Speed Up ◽

Energy Maps ◽

Simulation Time

Atomic force microscopy (AFM) has been an important tool for nanoscale imaging and characterization with atomic and subatomic resolution. Theoretical investigations are getting highly important for the interpretation of AFM images. Researchers have used molecular simulation to examine the AFM imaging mechanism. With a recent flurry of researches applying machine learning to AFM, AFM images obtained from molecular simulation have also been used as training data. However, the simulation is incredibly time consuming. In this paper, we apply super-resolution methods, including compressed sensing and deep learning methods, to reconstruct simulated images and to reduce simulation time. Several molecular simulation energy maps under different conditions are presented to demonstrate the performance of reconstruction algorithms. Through the analysis of reconstructed results, we find that both presented algorithms could complete the reconstruction with good quality and greatly reduce simulation time. Moreover, the super-resolution methods can be used to speed up the generation of training data and vary simulation resolution for AFM machine learning.

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