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  1. Article ; Online: 100 Years of the Lennard-Jones Potential.

    Schwerdtfeger, Peter / Wales, David J

    Journal of chemical theory and computation

    2024  

    Abstract: It is now 100 years since Lennard-Jones published his first paper introducing the now famous potential that bears his name. It is therefore timely to reflect on the many achievements, as well as the limitations, of this potential in the theory of atomic ... ...

    Abstract It is now 100 years since Lennard-Jones published his first paper introducing the now famous potential that bears his name. It is therefore timely to reflect on the many achievements, as well as the limitations, of this potential in the theory of atomic and molecular interactions, where applications range from descriptions of intermolecular forces to molecules, clusters, and condensed matter.
    Language English
    Publishing date 2024-04-26
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.4c00135
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Analysis and interpretation of first passage time distributions featuring rare events.

    Woods, Esmae J / Wales, David J

    Physical chemistry chemical physics : PCCP

    2024  Volume 26, Issue 3, Page(s) 1640–1657

    Abstract: In this contribution we consider theory and associated computational tools to treat the kinetics associated with competing pathways on multifunnel energy landscapes. Multifunnel landscapes are associated with molecular switches and multifunctional ... ...

    Abstract In this contribution we consider theory and associated computational tools to treat the kinetics associated with competing pathways on multifunnel energy landscapes. Multifunnel landscapes are associated with molecular switches and multifunctional materials, and are expected to exhibit multiple relaxation time scales and associated thermodynamic signatures in the heat capacity. Our focus here is on the first passage time distribution, which is encoded in a kinetic transition network containing all the locally stable states and the pathways between them. This network can be renormalised to reduce the dimensionality, while exactly conserving the mean first passage time and approximately conserving the full distribution. The structure of the reduced network can be visualised using disconnectivity graphs. We show how features in the first passage time distribution can be associated with specific kinetic traps, and how the appearance of competing relaxation time scales depends on the starting conditions. The theory is tested for two model landscapes and applied to an atomic cluster and a disordered peptide. Our most important contribution is probably the reconstruction of the full distribution for long time scales, where numerical problems prevent direct calculations. Here we combine accurate treatment of the mean first passage time with the reliable part of the distribution corresponding to faster time scales. Hence we now have a fundamental understanding of both thermodynamic and kinetic signatures of multifunnel landscapes.
    Language English
    Publishing date 2024-01-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d3cp04199a
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  3. Article ; Online: Dynamical Signatures of Multifunnel Energy Landscapes.

    Wales, David J

    The journal of physical chemistry letters

    2022  Volume 13, Issue 27, Page(s) 6349–6358

    Abstract: Multifunctional systems, such as molecular switches, exhibit multifunnel energy landscapes associated with the alternative functional states. In this contribution the multifunnel organization is decoded from dynamical signatures in the first passage time ...

    Abstract Multifunctional systems, such as molecular switches, exhibit multifunnel energy landscapes associated with the alternative functional states. In this contribution the multifunnel organization is decoded from dynamical signatures in the first passage time distribution between reactants and products. Characteristic relaxation rates are revealed by analyzing the kinetics as a function of the observation time scale, which scans the underlying distribution. Extracting the corresponding dynamical signatures provides direct insight into the organization of the molecular energy landscape, which will facilitate a rational design of target functionality. Examples are illustrated for multifunnel landscapes in biomolecular systems and an atomic cluster.
    MeSH term(s) Kinetics ; Thermodynamics
    Language English
    Publishing date 2022-07-08
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.2c01258
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  4. Article ; Online: Energy Landscapes and Heat Capacity Signatures for Monomers and Dimers of Amyloid-Forming Hexapeptides.

    Nicy / Wales, David J

    International journal of molecular sciences

    2023  Volume 24, Issue 13

    Abstract: Amyloid formation is a hallmark of various neurodegenerative disorders. In this contribution, energy landscapes are explored for various hexapeptides that are known to form amyloids. Heat capacity (CV) analysis at low temperature for these hexapeptides ... ...

    Abstract Amyloid formation is a hallmark of various neurodegenerative disorders. In this contribution, energy landscapes are explored for various hexapeptides that are known to form amyloids. Heat capacity (CV) analysis at low temperature for these hexapeptides reveals that the low energy structures contributing to the first heat capacity feature above a threshold temperature exhibit a variety of backbone conformations for amyloid-forming monomers. The corresponding control sequences do not exhibit such structural polymorphism, as diagnosed via end-to-end distance and a dihedral angle defined for the monomer. A similar heat capacity analysis for dimer conformations obtained using basin-hopping global optimisation shows clear features in end-to-end distance versus dihedral correlation plots, where amyloid-forming sequences exhibit a preference for larger end-to-end distances and larger positive dihedrals. These results hold true for sequences taken from tau, amylin, insulin A chain, a de novo designed peptide, and various control sequences. While there is a little overall correlation between the aggregation propensity and the temperature at which the low-temperature CV feature occurs, further analysis suggests that the amyloid-forming sequences exhibit the key CV feature at a lower temperature compared to control sequences derived from the same protein.
    MeSH term(s) Humans ; Hot Temperature ; Amyloid/chemistry ; Amyloidogenic Proteins ; Temperature ; Neurodegenerative Diseases
    Chemical Substances Amyloid ; Amyloidogenic Proteins
    Language English
    Publishing date 2023-06-25
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms241310613
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  5. Article ; Online: Stable and scalable computation of state visitation probabilities in finite Markov chains.

    Sharpe, Daniel J / Wales, David J

    The Journal of chemical physics

    2023  Volume 158, Issue 21

    Abstract: We report an algorithm based on renormalization to compute the probability that a particular state, or set thereof, is visited along the first passage or transition paths between two endpoint states of a finite Markov chain. The procedure is numerically ... ...

    Abstract We report an algorithm based on renormalization to compute the probability that a particular state, or set thereof, is visited along the first passage or transition paths between two endpoint states of a finite Markov chain. The procedure is numerically stable and does not require dense storage of the transition matrix.
    Language English
    Publishing date 2023-06-05
    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 10.1063/5.0154772
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Molecular Energy Landscapes of Hardware-Efficient Ansätze in Quantum Computing.

    Choy, Boy / Wales, David J

    Journal of chemical theory and computation

    2023  Volume 19, Issue 4, Page(s) 1197–1206

    Abstract: Rapid advances in quantum computing have opened up new opportunities for solving the central electronic structure problem in computational chemistry. In the noisy intermediate-scale quantum (NISQ) era, where qubit coherence times are limited, it is ... ...

    Abstract Rapid advances in quantum computing have opened up new opportunities for solving the central electronic structure problem in computational chemistry. In the noisy intermediate-scale quantum (NISQ) era, where qubit coherence times are limited, it is essential to exploit quantum algorithms with sufficiently short quantum circuits to maximize qubit efficiency. The procedural construction of hardware-efficient ansätze provides one approach to design such circuits. However, refining the accuracy of the global minimum by increasing circuit depth may lead to a proliferation of local minima that hinders global optimization. To investigate this phenomenon, we explore the energy landscapes of hardware-efficient circuits to identify ground-state energies of the hydrogen, lithium hydride, and beryllium hydride molecules. We also propose a simple dimensionality reduction procedure that reduces quantum gate depth while retaining high accuracy for the global minimum, simplifying the energy landscape, and hence speeding up optimization from both software and hardware perspectives.
    Language English
    Publishing date 2023-02-07
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.2c01057
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  7. Article ; Online: Multilevel Framework for Analysis of Protein Folding Involving Disulfide Bond Formation.

    Wesołowski, Patryk A / Wales, David J / Pracht, Philipp

    The journal of physical chemistry. B

    2024  Volume 128, Issue 13, Page(s) 3145–3156

    Abstract: In this study, a three-layered multicenter ONIOM approach is implemented to characterize the naive folding pathway of bovine pancreatic trypsin inhibitor (BPTI). Each layer represents a distinct level of theory, where the initial layer, encompassing the ... ...

    Abstract In this study, a three-layered multicenter ONIOM approach is implemented to characterize the naive folding pathway of bovine pancreatic trypsin inhibitor (BPTI). Each layer represents a distinct level of theory, where the initial layer, encompassing the entire protein, is modeled by a general all-atom force-field GFN-FF. An intermediate electronic structure layer consisting of three multicenter fragments is introduced with the state-of-the-art semiempirical tight-binding method GFN2-
    MeSH term(s) Animals ; Cattle ; Aprotinin/chemistry ; Cystine/chemistry ; Disulfides/chemistry ; Protein Folding ; Proteins
    Chemical Substances Aprotinin (9087-70-1) ; Cystine (48TCX9A1VT) ; Disulfides ; Proteins
    Language English
    Publishing date 2024-03-21
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.4c00104
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  8. Article: The Energy Landscape Perspective: Encoding Structure and Function for Biomolecules.

    Röder, Konstantin / Wales, David J

    Frontiers in molecular biosciences

    2022  Volume 9, Page(s) 820792

    Abstract: The energy landscape perspective is outlined with particular reference to biomolecules that perform multiple functions. We associate these multifunctional molecules with multifunnel energy landscapes, illustrated by some selected examples, where ... ...

    Abstract The energy landscape perspective is outlined with particular reference to biomolecules that perform multiple functions. We associate these multifunctional molecules with multifunnel energy landscapes, illustrated by some selected examples, where understanding the organisation of the landscape has provided new insight into function. Conformational selection and induced fit may provide alternative routes to realisation of multifunctionality, exploiting the possibility of environmental control and distinct binding modes.
    Language English
    Publishing date 2022-01-27
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2022.820792
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  9. Article ; Online: Energy Landscapes and Heat Capacity Signatures for Monomers and Dimers of Amyloid-Forming Hexapeptides

    Nicy / David J. Wales

    International Journal of Molecular Sciences, Vol 24, Iss 10613, p

    2023  Volume 10613

    Abstract: Amyloid formation is a hallmark of various neurodegenerative disorders. In this contribution, energy landscapes are explored for various hexapeptides that are known to form amyloids. Heat capacity ( ... C V ... ) analysis at low ... ...

    Abstract Amyloid formation is a hallmark of various neurodegenerative disorders. In this contribution, energy landscapes are explored for various hexapeptides that are known to form amyloids. Heat capacity ( <semantics> C V </semantics> ) analysis at low temperature for these hexapeptides reveals that the low energy structures contributing to the first heat capacity feature above a threshold temperature exhibit a variety of backbone conformations for amyloid-forming monomers. The corresponding control sequences do not exhibit such structural polymorphism, as diagnosed via end-to-end distance and a dihedral angle defined for the monomer. A similar heat capacity analysis for dimer conformations obtained using basin-hopping global optimisation shows clear features in end-to-end distance versus dihedral correlation plots, where amyloid-forming sequences exhibit a preference for larger end-to-end distances and larger positive dihedrals. These results hold true for sequences taken from tau, amylin, insulin A chain, a de novo designed peptide, and various control sequences. While there is a little overall correlation between the aggregation propensity and the temperature at which the low-temperature <semantics> C V </semantics> feature occurs, further analysis suggests that the amyloid-forming sequences exhibit the key <semantics> C V </semantics> feature at a lower temperature compared to control sequences derived from the same protein.
    Keywords energy landscapes ; amyloid formation ; hexapeptides ; heat capacity ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 511
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Global analysis of energy landscapes for materials modeling: A test case for C60.

    Csányi, Gábor / Morgan, John W R / Wales, David J

    The Journal of chemical physics

    2023  Volume 159, Issue 10

    Abstract: In this contribution, we employ computational tools from the energy landscape approach to test Gaussian Approximation Potentials (GAPs) for C60. In particular, we apply basin-hopping global optimization and explore the landscape starting from the low- ... ...

    Abstract In this contribution, we employ computational tools from the energy landscape approach to test Gaussian Approximation Potentials (GAPs) for C60. In particular, we apply basin-hopping global optimization and explore the landscape starting from the low-lying minima using discrete path sampling. We exploit existing databases of minima and transition states harvested from previous work using tight-binding potentials. We explore the energy landscape for the full range of structures and pathways spanning from the buckminsterfullerene global minimum up to buckybowls. In the initial GAP model, the fullerene part of the landscape is reproduced quite well. However, there are extensive families of C1@C59 and C2@C58 structures that lie lower in energy. We succeeded in refining the potential to remove these artifacts by simply including two minima from the C2@C58 families found by global landscape exploration. We suggest that the energy landscape approach could be used systematically to test and improve machine learning interatomic potentials.
    Language English
    Publishing date 2023-09-11
    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 10.1063/5.0167857
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