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Article ; Online: Accelerating Kinetics with Time-Reversal Path Sampling

Zhirong Liu

Molecules, Vol 28, Iss 24, p

2023 Volume 8147

Abstract: In comparison to numerous enhanced sampling methods for equilibrium thermodynamics, accelerating simulations for kinetics and nonequilibrium statistics are relatively rare and less effective. Here, we derive a time-reversal path sampling (tRPS) method ... ...

Abstract	In comparison to numerous enhanced sampling methods for equilibrium thermodynamics, accelerating simulations for kinetics and nonequilibrium statistics are relatively rare and less effective. Here, we derive a time-reversal path sampling (tRPS) method based on time reversibility to accelerate simulations for determining the transition rates between free-energy basins. It converts the difficult uphill path sampling into an easy downhill problem. This method is easy to implement, i.e., forward and backward shooting simulations with opposite initial velocities are conducted from random initial conformations within a transition-state region until they reach the basin minima, which are then assembled to give the distribution of transition paths efficiently. The effects of tRPS are demonstrated using a comparison with direct simulations of protein folding and unfolding, where tRPS is shown to give results consistent with direct simulations and increase the efficiency by up to five orders of magnitude. This approach is generally applicable to stochastic processes with microscopic reversibility, regardless of whether the variables are continuous or discrete.
Keywords	accelerated kinetics ; nonequilibrium statistics ; time reversibility ; enhanced sampling ; protein folding ; Organic chemistry ; QD241-441
Subject code	612
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Accelerating Kinetics with Time-Reversal Path Sampling.

Liu, Zhirong

Molecules (Basel, Switzerland)

2023 Volume 28, Issue 24

Abstract	In comparison to numerous enhanced sampling methods for equilibrium thermodynamics, accelerating simulations for kinetics and nonequilibrium statistics are relatively rare and less effective. Here, we derive a time-reversal path sampling (tRPS) method based on time reversibility to accelerate simulations for determining the transition rates between free-energy basins. It converts the difficult uphill path sampling into an easy downhill problem. This method is easy to implement, i.e., forward and backward shooting simulations with opposite initial velocities are conducted from random initial conformations within a transition-state region until they reach the basin minima, which are then assembled to give the distribution of transition paths efficiently. The effects of tRPS are demonstrated using a comparison with direct simulations of protein folding and unfolding, where tRPS is shown to give results consistent with direct simulations and increase the efficiency by up to five orders of magnitude. This approach is generally applicable to stochastic processes with microscopic reversibility, regardless of whether the variables are continuous or discrete.
Language	English
Publishing date	2023-12-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules28248147
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Book ; Online: Accelerating Kinetics with Time-reversal Path Sampling

Liu, Zhirong

2023

Abstract: In comparison to numerous enhanced sampling methods for equilbrium thermodynamics, accelerating simulations for kinetics and nonequilibrium statistics are relatively rare and less effective. Here we derive a time-reversal path sampling (tRPS) method ... ...

Abstract	In comparison to numerous enhanced sampling methods for equilbrium thermodynamics, accelerating simulations for kinetics and nonequilibrium statistics are relatively rare and less effective. Here we derive a time-reversal path sampling (tRPS) method based on the time reversibility to accelerate simulations for determining the transition rates between free-ernegy basins. It converts the difficult up-hill path sampling into an easy down-hill problem. The method is easy to implement, i.e., forward and backward shooting simulations with opposite initial velocities are conducted from random initial conformations within a transition-state region until they reach the basin minima, which are then assembled to give the distribution of transition paths efficiently. The effects of tRPS are demonstrated by comparison with direct simulations on protein folding and unfolding, where tRPS is shown to give results consistent with direct simulations and increase the efficiency by up to five orders of magnitude. The approach is generally applicable to stochatic processes with microscopic reversibility, no mater whether the variables are continuous or discrete. Comment: 11 pages, 10 figures; added some discussions and the supporting informations
Keywords	Physics - Chemical Physics
Subject code	612
Publishing date	2023-07-22
Publishing country	us
Document type	Book ; Online
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Article ; Online: Novel Piezoelectricity in Two-Dimensional Metallic/Semimetallic Materials with Out-of-Plane Polarization.

Wang, Zijian / Liu, Zhirong

The journal of physical chemistry letters

2023 Volume 14, Issue 33, Page(s) 7549–7555

Abstract: Normally, the good conductivity of metals and semimetals is incompatible with the piezoelectricity since the internal electric current will dismiss any polarization. However, here, we reveal that the out-of-plane piezoelectric effect can exist in two- ... ...

Abstract	Normally, the good conductivity of metals and semimetals is incompatible with the piezoelectricity since the internal electric current will dismiss any polarization. However, here, we reveal that the out-of-plane piezoelectric effect can exist in two-dimensional (2D) metallic/semimetallic materials due to their giant anisotropy. A method is developed to calculate the out-of-plane polarization in 2D systems, where the modern theory of polarization based on a Berry-phase approach is not applicable. Detailed calculation and analysis on a Dirac material, the FeB
Language	English
Publishing date	2023-08-17
Publishing country	United States
Document type	Journal Article
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.3c01796
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Article ; Online: Editorial

Daqian Liu / Zhirong Liu / Yun Wang / Limin Zhou

Frontiers in Environmental Science, Vol

Understanding heavy metal pollution and control in the environment around metal tailings

2023 Volume 11

Keywords	heavy metal ; liver fibrosis ; release ; reduction ; biochar ; Environmental sciences ; GE1-350
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Research progress on the correlation between MRI and impairment caused by cerebral small vessel disease: A review.

Wang, Yang / Liu, Zhirong

Medicine

2023 Volume 102, Issue 40, Page(s) e35389

Abstract: Cerebral small vessel disease (CSVD) is a chronic global brain disease mainly involving small blood vessels in the brain. The disease can be gradually aggravated with the increase of age, so it is the primary cause of brain dysfunction in the elderly. ... ...

Abstract	Cerebral small vessel disease (CSVD) is a chronic global brain disease mainly involving small blood vessels in the brain. The disease can be gradually aggravated with the increase of age, so it is the primary cause of brain dysfunction in the elderly. With the increasing aging of the world population and the high incidence of cerebrovascular risk factors, the incidence of CSVD is increasing day by day. CSVD is characterized by insidious onset, slow progression, diverse clinical manifestations, and difficult early diagnosis. CSVD can lead to cognitive impairment, gait impairment, affective impairment, and so on. however, it has not received enough attention from researchers in the past. In recent years, some studies have shown that CSVD patients have a high proportion of related impairment, which seriously affect patients daily life and social functions. Currently, no clear preventive measures or treatments exist to improve the condition. With the development of magnetic resonance imaging, CSVD has become more and more recognized and the detection rate has gradually improved. This paper reviews the research progress of magnetic resonance imaging and cognitive impairment, gait impairment, affective impairment, urination disorder, swallowing disorder, and other disorders to provide a useful reference for the early diagnosis and treatment of CSVD and expand new ideas.
MeSH term(s)	Humans ; Aged ; Brain/pathology ; Magnetic Resonance Imaging/methods ; Cognitive Dysfunction/diagnostic imaging ; Cognitive Dysfunction/etiology ; Risk Factors ; Brain Diseases/complications ; Cerebral Small Vessel Diseases/complications ; Cerebral Small Vessel Diseases/diagnostic imaging
Language	English
Publishing date	2023-10-06
Publishing country	United States
Document type	Review ; Journal Article
ZDB-ID	80184-7
ISSN	1536-5964 ; 0025-7974
ISSN (online)	1536-5964
ISSN	0025-7974
DOI	10.1097/MD.0000000000035389
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Article ; Online: Dirac cones in bipartite square-octagon lattice: A theoretical approach.

He, Junwei / Liu, Zhirong

The Journal of chemical physics

2023 Volume 159, Issue 4

Abstract: Dirac cones are difficult to achieve in a square lattice with full symmetry. Here, we have theoretically investigated a bipartite tetragonal lattice composed of tetragons and octagons using both Tight-Binding (TB) model and density functional theory (DFT) ...

Abstract	Dirac cones are difficult to achieve in a square lattice with full symmetry. Here, we have theoretically investigated a bipartite tetragonal lattice composed of tetragons and octagons using both Tight-Binding (TB) model and density functional theory (DFT) calculations. The TB model predicts that the system exhibits nodal line semi-metallic properties when the on-site energies of all atoms are identical. When the on-site energies differ, the formation of an elliptical Dirac cone is predicted. Its physical properties (anisotropy, tilting, merging, and emerging) can be regulated by the hopping energies. An exact analytical formula is derived to determine the position of the Dirac point by the TB parameters, and a criterion for the existence of Dirac cones is obtained. The "divide-and-coupling" method is applied to understand the origin of the Dirac cone, which involves dividing the bands into several groups and examining the couplings among inter-groups and intra-groups. Various practical systems computed by DFT methods, e.g., t-BN, t-Si, 4,12,2-graphyne, and t-SiC, are also examined, and they all possess nodal lines or Dirac cones as predicted by the TB model. The results provide theoretical foundation for designing novel Dirac materials with tetragonal symmetry.
Language	English
Publishing date	2023-07-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0160658
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Article ; Online: Internet use, physical activity and depressive symptoms in older adults: A cross-lagged panel analysis.

Liu, Ningning / Wang, Yumeng / Li, Zhirong

Journal of affective disorders

2024 Volume 350, Page(s) 937–945

Abstract: Background: Existing cross-sectional studies suggest a strong positive association between Internet use, physical activity, and mental health in older adults; however, longitudinal studies reporting the relationship between Internet use, physical ... ...

Abstract	Background: Existing cross-sectional studies suggest a strong positive association between Internet use, physical activity, and mental health in older adults; however, longitudinal studies reporting the relationship between Internet use, physical activity, and levels of depressive symptoms in older adults are lacking. This study aimed to examine the bidirectional relationship between Internet use and depressive symptoms in older adults and its underlying mechanisms. Methods: We used two waves of follow-up data (2016 and 2018) from the China Family Panel Studies, including 5837 participants aged 60 years or above. The bidirectional relationship between Internet usage time and depressive symptoms was examined using a cross-lagged model. The mediating role of physical exercise was examined using a half-longitudinal mediation model. Results: The results revealed a bidirectional relationship between Internet use time, frequency of physical activity, and depressive symptoms. Longer Internet use predicted lower levels of depressive symptoms, and the frequency of physical activity mediated the longitudinal relationship between Internet use and depressive symptoms in older adults. Limitations: First, our study used self-report-based variables. Second, our study did not obtain the specific timing of the application of various functions of the Internet and the intensity of physical activity among older adults. Finally, based on the availability of data, our study involved only two waves of data. This may not be sufficient for a full longitudinal mediation effect test. Conclusions: Internet use and depressive symptoms were interrelated over time among older adults. The frequency of physical activity was a mediator of Internet use and depressive symptoms. This underscores the importance of Internet-based technologies to enable healthy living and prevent depression and loneliness in older adults.
MeSH term(s)	Humans ; Aged ; Internet Use ; Depression/psychology ; Cross-Sectional Studies ; Exercise/psychology ; Longitudinal Studies
Language	English
Publishing date	2024-01-24
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	135449-8
ISSN	1573-2517 ; 0165-0327
ISSN (online)	1573-2517
ISSN	0165-0327
DOI	10.1016/j.jad.2024.01.201
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Article ; Online: Isolation and identification of a high-efficiency hexavalent uranium adsorption strain and preliminary study of the influencing factors and adsorption mechanism.

Wu, Faming / Li, Xiang / Wei, Peng / Liu, Zhirong

Environmental science and pollution research international

2024 Volume 31, Issue 17, Page(s) 26112–26122

Abstract: In this study, a bacterial strain Chryseobacterium bernardetii WK-3 was isolated from the rhizosphere soil of a uranium tailings in Southern China. It can efficiently adsorb hexavalent uranium with an adsorption ratio of 92.3%. The influence of different ...

Abstract	In this study, a bacterial strain Chryseobacterium bernardetii WK-3 was isolated from the rhizosphere soil of a uranium tailings in Southern China. It can efficiently adsorb hexavalent uranium with an adsorption ratio of 92.3%. The influence of different environmental conditions on the adsorption ratio of Chryseobacterium bernardetii strain WK-3 was investigated, and the adsorption mechanism was preliminarily discussed by scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS). The results showed that the optimal adsorption conditions for U(VI) by Chryseobacterium bernardetii strain WK-3 were pH = 5, temperature 30 ℃, NaCl concentration 1%, and inoculation volume 10%. When the initial concentration of U was 50 ~ 150 mg/L, the adsorption capacity of Chryseobacterium bernardetii strain WK-3 to U(VI) reached the maximum and maintained the equilibrium at 44 h. SEM-EDS results showed that phosphorus in cells participates in the interaction of uranyl ions, which may indicate that phosphate was produced during cell metabolism and was further combined to form U(VI)-phosphate minerals. In summary, Chryseobacterium bernardetii strain WK-3 would be a promising alternative for environmental uranium contamination remediation.
MeSH term(s)	Uranium/analysis ; Adsorption ; Soil ; Phosphates ; Kinetics ; Hydrogen-Ion Concentration ; Chryseobacterium
Chemical Substances	Uranium (4OC371KSTK) ; Soil ; Phosphates
Language	English
Publishing date	2024-03-16
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-024-32934-6
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Article ; Online: Robust Federated Learning: Maximum Correntropy Aggregation Against Byzantine Attacks.

Luan, Zhirong / Li, Wenrui / Liu, Meiqin / Chen, Badong

IEEE transactions on neural networks and learning systems

2024 Volume PP

Abstract: As an emerging decentralized machine learning technique, federated learning organizes collaborative training and preserves the privacy and security of participants. However, untrustworthy devices, typically Byzantine attackers, pose a significant ... ...

Abstract	As an emerging decentralized machine learning technique, federated learning organizes collaborative training and preserves the privacy and security of participants. However, untrustworthy devices, typically Byzantine attackers, pose a significant challenge to federated learning since they can upload malicious parameters to corrupt the global model. To defend against such attacks, we propose a novel robust aggregation method-maximum correntropy aggregation (MCA), which applies the maximum correntropy criterion (MCC) to derive a central value from parameters. Different from the previous use of MCC for denoising, we utilize it as a similarity metric to measure parameter distribution and aggregate a robust center. Correntropy in MCC, with all even-order moments of the parameter, contains high-order statistical properties, which allows for a comprehensive capture of parameter characteristics, thus helping to prevent interference from attackers. Meanwhile, correntropy extracts information from the parameters themselves, without requiring the proportion of malicious attackers. Through the fixed-point iteration, we solve the optimization objective, demonstrating the linear convergence of the iteration formula. Theoretical analysis reveals the robustness aggregation property of MCA and the error bound between MCA and the global optimal solution, with linear convergence to the optimal solution neighborhood. By performing independent identically distribution (IID) and non-IID experiments on three different datasets, we show that MCA exhibits significant robustness under mainstream attacks, whereas other methods cannot withstand all of them.
Language	English
Publishing date	2024-04-23
Publishing country	United States
Document type	Journal Article
ISSN	2162-2388
ISSN (online)	2162-2388
DOI	10.1109/TNNLS.2024.3383294
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