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Article ; Online: Understanding the "Berg limit": the 65° contact angle as the universal adhesion threshold of biomatter.

Kanduč, Matej / Schneck, Emanuel / Netz, Roland R

Physical chemistry chemical physics : PCCP

2024 Volume 26, Issue 2, Page(s) 713–723

Abstract: Surface phenomena in aqueous environments such as long-range hydrophobic attraction, macromolecular adhesion, and even biofouling are predominantly influenced by a fundamental parameter-the water contact angle. The minimal contact angle required for ... ...

Abstract	Surface phenomena in aqueous environments such as long-range hydrophobic attraction, macromolecular adhesion, and even biofouling are predominantly influenced by a fundamental parameter-the water contact angle. The minimal contact angle required for these and related phenomena to occur has been repeatedly reported to be around 65° and is commonly referred to as the "Berg limit." However, the universality of this specific threshold across diverse contexts has remained puzzling. In this perspective article, we aim to rationalize the reoccurrence of this enigmatic contact angle. We show that the relevant scenarios can be effectively conceptualized as three-phase problems involving the surface of interest, water, and a generic oil-like material that is representative of the nonpolar constituents within interacting entities. Our analysis reveals that attraction and adhesion emerge when substrates display an underwater oleophilic character, corresponding to a "hydrophobicity under oil", which occurs for contact angles above approximately 65°. This streamlined view provides valuable insights into macromolecular interactions and holds implications for technological applications.
Language	English
Publishing date	2024-01-03
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d3cp05084j
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Accurate Memory Kernel Extraction from Discretized Time-Series Data.

Tepper, Lucas / Dalton, Benjamin / Netz, Roland R

Journal of chemical theory and computation

2024 Volume 20, Issue 8, Page(s) 3061–3068

Abstract: Memory effects emerge as a fundamental consequence of dimensionality reduction when low-dimensional observables are used to describe the dynamics of complex many-body systems. In the context of molecular dynamics (MD) data analysis, accounting for memory ...

Abstract	Memory effects emerge as a fundamental consequence of dimensionality reduction when low-dimensional observables are used to describe the dynamics of complex many-body systems. In the context of molecular dynamics (MD) data analysis, accounting for memory effects using the framework of the generalized Langevin equation (GLE) has proven efficient, accurate, and insightful, particularly when working with high-resolution time series data. However, in experimental systems, high-resolution data are often unavailable, raising questions about the impact of the data resolution on the estimated GLE parameters. This study demonstrates that direct memory extraction from time series data remains accurate when the discretization time is below the memory time. To obtain memory functions reliably, even when the discretization time exceeds the memory time, we introduce a Gaussian Process Optimization (GPO) scheme. This scheme minimizes the deviation of discretized two-point correlation functions between time series data and GLE simulations and is able to estimate accurate memory kernels as long as the discretization time stays below the longest time scale in the data, typically the barrier crossing time.
Language	English
Publishing date	2024-04-11
Publishing country	United States
Document type	Journal Article
ISSN	1549-9626
ISSN (online)	1549-9626
DOI	10.1021/acs.jctc.3c01289
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Article ; Online: Approach to equilibrium and nonequilibrium stationary distributions of interacting many-particle systems that are coupled to different heat baths.

Netz, Roland R

Physical review. E

2020 Volume 101, Issue 2-1, Page(s) 22120

Abstract: A Hamiltonian-based model of many harmonically interacting massive particles that are subject to linear friction and coupled to heat baths at different temperatures is used to study the dynamic approach to equilibrium and nonequilibrium stationary states. ...

Abstract	A Hamiltonian-based model of many harmonically interacting massive particles that are subject to linear friction and coupled to heat baths at different temperatures is used to study the dynamic approach to equilibrium and nonequilibrium stationary states. An equilibrium system is here defined as a system whose stationary distribution equals the Boltzmann distribution, the relation of this definition to the conditions of detailed balance and vanishing probability current is discussed both for underdamped as well as for overdamped systems. Based on the exactly calculated dynamic approach to the stationary distribution, the functional that governs this approach, which is called the free entropy S_{free}(t), is constructed. For the stationary distribution S_{free}(t) becomes maximal and its time derivative, the free entropy production S[over ̇]_{free}(t), is minimal and vanishes. Thus, S_{free}(t) characterizes equilibrium as well as nonequilibrium stationary distributions by their extremal and stability properties. For an equilibrium system, i.e., if all heat baths have the same temperature, the free entropy equals the negative free energy divided by temperature and thus corresponds to the Massieu function which was previously introduced in an alternative formulation of statistical mechanics. Using a systematic perturbative scheme for calculating velocity and position correlations in the overdamped massless limit, explicit results for few particles are presented: For two particles localization in position and momentum space is demonstrated in the nonequilibrium stationary state, indicative of a tendency to phase separate. For three elastically interacting particles heat flows from a particle coupled to a cold reservoir to a particle coupled to a warm reservoir if the third reservoir is sufficiently hot. This does not constitute a violation of the second law of thermodynamics, but rather demonstrates that a particle in such a nonequilibrium system is not characterized by an effective temperature which equals the temperature of the heat bath it is coupled to. Active particle models can be described in the same general framework, which thereby allows us to characterize their entropy production not only in the stationary state but also in the approach to the stationary nonequilibrium state. Finally, the connection to nonequilibrium thermodynamics formulations that include the reservoir entropy production is discussed.
Language	English
Publishing date	2020-03-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.101.022120
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Article ; Online: Mechanisms of Airborne Infection via Evaporating and Sedimenting Droplets Produced by Speaking.

Netz, Roland R

The journal of physical chemistry. B

2020 Volume 124, Issue 33, Page(s) 7093–7101

Abstract: For estimating the infection risk from virus-containing airborne droplets, it is crucial to consider the interplay of all relevant physical-chemical effects that affect droplet evaporation and sedimentation times. For droplet radii in the range 70 nm < ...

Abstract	For estimating the infection risk from virus-containing airborne droplets, it is crucial to consider the interplay of all relevant physical-chemical effects that affect droplet evaporation and sedimentation times. For droplet radii in the range 70 nm <
MeSH term(s)	Aerosols ; Air Microbiology ; Algorithms ; Betacoronavirus ; COVID-19 ; Coronavirus Infections/transmission ; Diffusion ; Humans ; Pandemics ; Particle Size ; Pneumonia, Viral/transmission ; Risk Assessment ; SARS-CoV-2 ; Speech ; Water
Chemical Substances	Aerosols ; Water (059QF0KO0R)
Keywords	covid19
Language	English
Publishing date	2020-07-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.0c05229
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Article ; Online: Non-Markovian Modeling of Nonequilibrium Fluctuations and Dissipation in Active Viscoelastic Biomatter.

Abbasi, Amir / Netz, Roland R / Naji, Ali

Physical review letters

2023 Volume 131, Issue 22, Page(s) 228202

Abstract: Based on a Hamiltonian that incorporates the elastic coupling between a tracer particle and the embedding active viscoelastic biomatter, we derive a generalized non-Markovian Langevin model for the nonequilibrium mechanical tracer response. Our ... ...

Abstract	Based on a Hamiltonian that incorporates the elastic coupling between a tracer particle and the embedding active viscoelastic biomatter, we derive a generalized non-Markovian Langevin model for the nonequilibrium mechanical tracer response. Our analytical expressions for the frequency-dependent tracer response function and the tracer positional autocorrelation function agree quantitatively with experimental data for red blood cells and actomyosin networks with and without adenosine triphosphate over the entire frequency range and in particular reproduce the low-frequency violation of the fluctuation-dissipation theorem. The viscoelastic power laws, the elastic constants and effective friction coefficients extracted from the experimental data allow straightforward physical interpretation.
Language	English
Publishing date	2023-12-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.131.228202
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Article ; Online: Fluctuation-dissipation relation and stationary distribution of an exactly solvable many-particle model for active biomatter far from equilibrium.

Netz, Roland R

The Journal of chemical physics

2018 Volume 148, Issue 18, Page(s) 185101

Abstract: An exactly solvable, Hamiltonian-based model of many massive particles that are coupled by harmonic potentials and driven by stochastic non-equilibrium forces is introduced. The stationary distribution and the fluctuation-dissipation relation are derived ...

Abstract	An exactly solvable, Hamiltonian-based model of many massive particles that are coupled by harmonic potentials and driven by stochastic non-equilibrium forces is introduced. The stationary distribution and the fluctuation-dissipation relation are derived in closed form for the general non-equilibrium case. Deviations from equilibrium are on one hand characterized by the difference of the obtained stationary distribution from the Boltzmann distribution; this is possible because the model derives from a particle Hamiltonian. On the other hand, the difference between the obtained non-equilibrium fluctuation-dissipation relation and the standard equilibrium fluctuation-dissipation theorem allows us to quantify non-equilibrium in an alternative fashion. Both indicators of non-equilibrium behavior, i.e., deviations from the Boltzmann distribution and deviations from the equilibrium fluctuation-dissipation theorem, can be expressed in terms of a single non-equilibrium parameter α that involves the ratio of friction coefficients and random force strengths. The concept of a non-equilibrium effective temperature, which can be defined by the relation between fluctuations and the dissipation, is by comparison with the exactly derived stationary distribution shown not to hold, even if the effective temperature is made frequency dependent. The analysis is not confined to close-to-equilibrium situations but rather is exact and thus holds for arbitrarily large deviations from equilibrium. Also, the suggested harmonic model can be obtained from non-linear mechanical network systems by an expansion in terms of suitably chosen deviatory coordinates; the obtained results should thus be quite general. This is demonstrated by comparison of the derived non-equilibrium fluctuation dissipation relation with experimental data on actin networks that are driven out of equilibrium by energy-consuming protein motors. The comparison is excellent and allows us to extract the non-equilibrium parameter α from experimental spectral response and fluctuation data.
Language	English
Publishing date	2018-05-14
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	10.1063/1.5020654
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Book ; Online: Accurate Memory Kernel Extraction from Discretized Time Series Data

Tepper, Lucas / Dalton, Benjamin / Netz, Roland R.

2024

Abstract	Memory effects emerge as a fundamental consequence of dimensionality reduction when low-dimensional observables are used to describe the dynamics of complex many-body systems. In the context of molecular dynamics (MD) data analysis, accounting for memory effects using the framework of the generalized Langevin equation (GLE) has proven efficient, accurate and insightful, particularly when working with high-resolution time series data. However, in experimental systems, high-resolution data is often unavailable, raising questions about the impact of the data resolution on the estimated GLE parameters. This study demonstrates that direct memory extraction remains accurate when the discretization time is below the memory time. To obtain memory functions reliably even when the discretization time exceeds the memory time, we introduce a Gaussian Process Optimization (GPO) scheme. This scheme minimizes the deviation of discretized two-point correlation functions between MD and GLE simulations and is able to estimate accurate memory kernels as long as the discretization time stays below the longest time scale in the data, typically the barrier crossing time.
Keywords	Physics - Data Analysis ; Statistics and Probability ; Physics - Computational Physics
Subject code	612
Publishing date	2024-01-17
Publishing country	us
Document type	Book ; Online
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Article ; Online: Estimating computational limits on theoretical descriptions of biological cells.

Netz, Roland R / Eaton, William A

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 6

Abstract: There has been much success recently in theoretically simulating parts of complex biological systems on the molecular level, with the goal of first-principles modeling of whole cells. However, there is the question of whether such simulations can be ... ...

Abstract	There has been much success recently in theoretically simulating parts of complex biological systems on the molecular level, with the goal of first-principles modeling of whole cells. However, there is the question of whether such simulations can be performed because of the enormous complexity of cells. We establish approximate equations to estimate computation times required to simulate highly simplified models of cells by either molecular dynamics calculations or by solving molecular kinetic equations. Our equations place limits on the complexity of cells that can be theoretically understood with these two methods and provide a first step in developing what can be considered biological uncertainty relations for molecular models of cells. While a molecular kinetics description of the genetically simplest bacterial cell may indeed soon be possible, neither theoretical description for a multicellular system, such as the human brain, will be possible for many decades and may never be possible even with quantum computing.
MeSH term(s)	Computing Methodologies ; Humans ; Kinetics ; Models, Biological ; Molecular Dynamics Simulation/standards ; Quantum Theory
Language	English
Publishing date	2021-01-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2022753118
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Article: Water evaporation from solute-containing aerosol droplets: Effects of internal concentration and diffusivity profiles and onset of crust formation.

Rezaei, Majid / Netz, Roland R

Physics of fluids (Woodbury, N.Y. : 1994)

2021 Volume 33, Issue 9, Page(s) 91901

Abstract: The evaporation of droplets is an important process not only in industrial and scientific applications, but also in the airborne transmission of viruses and other infectious agents. We derive analytical and semi-analytical solutions of the coupled heat ... ...

Abstract	The evaporation of droplets is an important process not only in industrial and scientific applications, but also in the airborne transmission of viruses and other infectious agents. We derive analytical and semi-analytical solutions of the coupled heat and mass diffusion equations within a spherical droplet and in the ambient vapor phase that describe the evaporation process of aqueous free droplets containing nonvolatile solutes. Our results demonstrate that the solute-induced water vapor-pressure reduction considerably slows down the evaporation process and dominates the solute-concentration dependence of the droplet evaporation time. The evaporation-induced enhanced solute concentration near the droplet surface, which is accounted for using a two-stage evaporation description, is found to further slow-down the drying process. On the other hand, the presence of solutes is found to produce a lower limit for the droplet size that can be reached by evaporation and, also, to reduce evaporation cooling of the droplet, which tend to decrease the evaporation time. Overall, the first two effects are dominant, meaning that the droplet evaporation time increases in the presence of solutes. Local variation of the water diffusivity inside the droplet near its surface, which is a consequence of the solute-concentration dependence of the diffusion coefficient, does not significantly change the evaporation time. Crust formation on the droplet surface increases the final equilibrium size of the droplet by producing a hollow spherical particle, the outer radius of which is determined as well.
Language	English
Publishing date	2021-09-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	1472743-2
ISSN	1089-7666 ; 1070-6631
ISSN (online)	1089-7666
ISSN	1070-6631
DOI	10.1063/5.0060080
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Article: Airborne virus transmission via respiratory droplets: Effects of droplet evaporation and sedimentation.

Rezaei, Majid / Netz, Roland R

Current opinion in colloid & interface science

2021 Volume 55, Page(s) 101471

Abstract: Airborne transmission is considered as an important route for the spread of infectious diseases, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and is primarily determined by the droplet sedimentation time, that is, the time ... ...

Abstract	Airborne transmission is considered as an important route for the spread of infectious diseases, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and is primarily determined by the droplet sedimentation time, that is, the time droplets spend in air before reaching the ground. Evaporation increases the sedimentation time by reducing the droplet mass. In fact, small droplets can, depending on their solute content, almost completely evaporate during their descent to the ground and remain airborne as so-called droplet nuclei for a long time. Considering that viruses possibly remain infectious in aerosols for hours, droplet nuclei formation can substantially increase the infectious viral air load. Accordingly, the physical-chemical factors that control droplet evaporation and sedimentation times and play important roles in determining the infection risk from airborne respiratory droplets are reviewed in this article.
Language	English
Publishing date	2021-05-29
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2019683-0
ISSN	1359-0294
ISSN	1359-0294
DOI	10.1016/j.cocis.2021.101471
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