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Article ; Online: Fickian Yet Non-Gaussian Nanoscopic Lipid Diffusion in the Raft-Mimetic Membrane.

Erimban, Shakkira / Daschakraborty, Snehasis

The journal of physical chemistry. B

2023 Volume 127, Issue 22, Page(s) 4939–4951

Abstract: Past experiments rationalized the observed dynamic heterogeneity and non-Gaussian diffusion in living cell membranes in terms of slow-active remodeling of the underlying cortical actin network. In this work, we demonstrate that the nanoscopic dynamic ... ...

Abstract	Past experiments rationalized the observed dynamic heterogeneity and non-Gaussian diffusion in living cell membranes in terms of slow-active remodeling of the underlying cortical actin network. In this work, we demonstrate that the nanoscopic dynamic heterogeneity can also be explained via the lipid raft hypothesis, which postulates a phase separation between liquid-ordered (Lo) and liquid-disordered (Ld) nanodomains. Non-Gaussian displacement distribution is observed in the Lo domain for a long time, even when the mean square displacement becomes Fickian. This Fickian yet non-Gaussian diffusion is found particularly in the Lo/Ld interface consistent with the "diffusing diffusion" picture. A translational jump-diffusion model, previously employed to explain the diffusion-viscosity decoupling in supercooled water, is used here to quantitatively explain the long-term dynamic heterogeneity where a strong correlation between translational jump and non-Gaussian diffusion is observed. Therefore, this study proposes a novel approach to elucidate the dynamic heterogeneity and non-Gaussian diffusion in the cell membrane crucial for various cell membrane functionalities.
Language	English
Publishing date	2023-05-25
Publishing country	United States
Document type	Journal Article
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.3c00019
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Article ; Online: Homeoviscous Adaptation of the Lipid Membrane of a Soil Bacterium Surviving under Diurnal Temperature Variation: A Molecular Simulation Perspective.

Erimban, Shakkira / Daschakraborty, Snehasis

The journal of physical chemistry. B

2022 Volume 126, Issue 39, Page(s) 7638–7650

Abstract: A recent experiment has reported the lipidome remodeling of a soil-based plant-associated ... ...

Abstract	A recent experiment has reported the lipidome remodeling of a soil-based plant-associated bacterium
MeSH term(s)	Bacteria ; Lipids ; Membranes ; Soil ; Temperature
Chemical Substances	Lipids ; Soil
Language	English
Publishing date	2022-09-27
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.2c01359
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Article ; Online: How does excess phenylalanine affect the packing density and fluidity of a lipid membrane?

Erimban, Shakkira / Daschakraborty, Snehasis

Physical chemistry chemical physics : PCCP

2021 Volume 23, Issue 48, Page(s) 27294–27303

Abstract: Phenylketonuria (PKU) is an autosomal recessive error of phenylalanine (Phe) metabolism, where untreated Phe becomes cytotoxic. Previous experiments found that excess Phe decreases the packing density and increases the fluidity and permeability of a ... ...

Abstract	Phenylketonuria (PKU) is an autosomal recessive error of phenylalanine (Phe) metabolism, where untreated Phe becomes cytotoxic. Previous experiments found that excess Phe decreases the packing density and increases the fluidity and permeability of a lipid membrane. It was proposed that Phe forms cytotoxic nanoscopic amyloid-like fibrils. In another study, the Phe fibrils were not visible near the lipid membrane. So, what leads to the deleterious effect of Phe on the lipid membrane? We put forward a molecular mechanism for the observed effect of excess Phe on the lipid membrane using all-atom molecular dynamics simulation. This study suggests that Phe monomers spontaneously intercalate into the membrane and form small hydrogen-bonded clusters, some of which locally perturb the membrane. These local effects result in an overall reduction in the membrane packing density, enhancement of membrane fluidity, and an increase of water permeability, observed in experiments. The present study does not observe any effect of the nanoscopic fibrillar structure of Phe on the membrane. This study, therefore, provides alternative insights into the excess Phe cytotoxicity in PKU disease.
MeSH term(s)	Hydrogen Bonding ; Membrane Lipids/chemistry ; Molecular Dynamics Simulation ; Permeability ; Phenylalanine/chemistry ; Water/chemistry
Chemical Substances	Membrane Lipids ; Water (059QF0KO0R) ; Phenylalanine (47E5O17Y3R)
Language	English
Publishing date	2021-12-15
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/d1cp05004d
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Article ; Online: Elucidating the relationship between red fluorescence and structural dynamics of carbon dots dispersed in different solvents.

Mandal, Saptarshi / Erimban, Shakkira / Banerjee, Subhrajeet / Daschakraborty, Snehasis / Das, Prolay

Physical chemistry chemical physics : PCCP

2023 Volume 25, Issue 35, Page(s) 23645–23657

Abstract: The mechanism of intrinsic fluorescence of carbon dots (CDs), the latest nanomaterial from the carbon family, was supposedly deciphered through multiple theories. However, the much sought-after persistent red emission of CDs as a foreseeable consequence ... ...

Abstract	The mechanism of intrinsic fluorescence of carbon dots (CDs), the latest nanomaterial from the carbon family, was supposedly deciphered through multiple theories. However, the much sought-after persistent red emission of CDs as a foreseeable consequence of experiments remains elusive prompting the question of whether tuning of the red emission of CDs is a predictable outcome or a serendipitous coincidence. Herein, we tried to decode the same by exploring Alizarin Red S (ARS)-based red emitting CDs in different solvents with wisely chosen analytical tools. The findings are aptly supported by molecular dynamics studies through an experimental intuition-driven model-building approach. Parallel interception of the CDs with powder X-ray diffraction (pXRD) and photophysical spectroscopic studies revealed an important relationship between the solvent and CDs. Tautomerism, a well-known phenomenon with chemical entities, was found to be operative for CDs that greatly influence the Stokes shift and ultimately the fluorescence outcome. Most importantly, pXRD studies established the turbostratism of the CDs where the well-ordered graphitic structure of CDs gets disrupted with solvent molecules. The extent of such disruption is a function of solvent and CD composition that plays a formidable role in obtaining red fluorescence. Thus, for the first time, we demonstrate that the red emission of CDs is related to its structural integrity and if taken care of could be sustained, a tremendously desirable outcome for relevant applications.
Language	English
Publishing date	2023-09-13
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/d3cp02498a
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Article ; Online: Cryostabilization of the Cell Membrane of a Psychrotolerant Bacteria via Homeoviscous Adaptation.

Erimban, Shakkira / Daschakraborty, Snehasis

The journal of physical chemistry letters

2020 Volume 11, Issue 18, Page(s) 7709–7716

Abstract: Homeoviscous adaptation (maintenance of a critical balance between the saturated and unsaturated lipids) of the cell membrane of psychrotolerant bacteria is essential to protect them against freeze-thaw cycle. But how does the homeoviscous adaptation ... ...

Abstract	Homeoviscous adaptation (maintenance of a critical balance between the saturated and unsaturated lipids) of the cell membrane of psychrotolerant bacteria is essential to protect them against freeze-thaw cycle. But how does the homeoviscous adaptation protect the cell membrane during cold stress? In this Letter, we answer this question using a coarse-grained molecular dynamics simulation technique. On the basis of the reported fatty acid profiles of psychrotolerant bacteria at different temperatures, multiple lipid membranes are simulated at a wide range of temperatures between 250 and 300 K. We explicate how the homeoviscous adaptation minimizes the effect of cold stress on the structure and fluidity of the membrane. Partial freezing of the saturated lipid domain occurs with the self-aggregation of saturated and unsaturated lipids near the melting temperature of the unadapted lipid membrane. The gel-like phase provides necessary local packing density that can be sensed by sensor proteins responsible for the homeoviscous adaptation.
MeSH term(s)	Adaptation, Physiological ; Cell Membrane/chemistry ; Flavobacteriaceae/chemistry ; Flavobacteriaceae/cytology ; Lipids/chemistry ; Temperature
Chemical Substances	Lipids
Language	English
Publishing date	2020-09-01
Publishing country	United States
Document type	Journal Article
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.0c01675
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Article ; Online: Translocation of a hydroxyl functionalized carbon dot across a lipid bilayer: an all-atom molecular dynamics simulation study.

Erimban, Shakkira / Daschakraborty, Snehasis

Physical chemistry chemical physics : PCCP

2020 Volume 22, Issue 11, Page(s) 6335–6350

Abstract: The major applications of carbon dots (CDs) (e.g. bio-imaging and targeted drug delivery) necessitate the latter to permeate across the lipid bilayer membrane. Unfortunately, the mechanism of permeation is poorly understood. Between the two possible ... ...

Abstract	The major applications of carbon dots (CDs) (e.g. bio-imaging and targeted drug delivery) necessitate the latter to permeate across the lipid bilayer membrane. Unfortunately, the mechanism of permeation is poorly understood. Between the two possible routes for permeation of a nanoparticle like CDs-an endocytic pathway and direct passive permeation-the endocytic path is known to be more common, despite the fact that the passive permeation is preferred over the endocytosis for targeted drug delivery. Here, we have focused on the direct permeation of a hydroxyl functionalized CD across the POPC lipid bilayer membrane using all-atom MD simulations. We have estimated the free energy profile for the translocation of the CD across the lipid bilayer, with a barrier height of ∼170 kJ mol
MeSH term(s)	Carbon/chemistry ; Carbon/metabolism ; Drug Delivery Systems ; Hydroxylation ; Lipid Bilayers/metabolism ; Molecular Dynamics Simulation
Chemical Substances	Lipid Bilayers ; Carbon (7440-44-0)
Language	English
Publishing date	2020-03-05
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/c9cp05999g
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Article ; Online: Investigating the Vapor-Phase Adsorption of Aroma Molecules on the Water-Vapor Interface using Molecular Dynamics Simulations.

Sharma, Tonmoy / Erimban, Shakkira / Azad, Rajnish / Nam, Youngsuk / Raj, Rishi / Daschakraborty, Snehasis

Langmuir : the ACS journal of surfaces and colloids

2023 Volume 39, Issue 49, Page(s) 17889–17902

Abstract: Surfactants are amphiphilic additives primarily used to reduce the surface tension of water and manipulate its wettability on various surfaces. Recent reports suggest that volatile surfactants, such as aroma molecules, diffuse more quickly to the ... ...

Abstract	Surfactants are amphiphilic additives primarily used to reduce the surface tension of water and manipulate its wettability on various surfaces. Recent reports suggest that volatile surfactants, such as aroma molecules, diffuse more quickly to the interface from the vapor-phase than conventional surfactants typically used in the aqueous phase. The ability to adsorb from the vapor phase, in addition to their use as cosurfactants, expands the potential applications of volatile surfactants, particularly in situations where adding surfactants from the liquid phase is difficult. Here, we present a molecular level understanding of the adsorption kinetics of linalool, a common aroma molecule, on the water interface using molecular dynamics simulations. We note that the value of surface tension while adsorption from vapor and liquid phases is dependent only on the surface coverage. A minimum surface tension of 32 ± 1.8 mN/m is obtained in both cases at a maximum surface coverage of 4.88 μmol/m
Language	English
Publishing date	2023-11-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	2005937-1
ISSN	1520-5827 ; 0743-7463
ISSN (online)	1520-5827
ISSN	0743-7463
DOI	10.1021/acs.langmuir.3c02531
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Article ; Online: Understanding the Origin of the Breakdown of the Stokes-Einstein Relation in Supercooled Water at Different Temperature-Pressure Conditions.

Dubey, Vikas / Erimban, Shakkira / Indra, Sandipa / Daschakraborty, Snehasis

The journal of physical chemistry. B

2019 Volume 123, Issue 47, Page(s) 10089–10099

Abstract: A recent experiment has measured the viscosity of water down to approximately 244 K and up to 300 MPa. The correct viscosity and translational diffusivity data at various temperature-pressure ( ...

Abstract	A recent experiment has measured the viscosity of water down to approximately 244 K and up to 300 MPa. The correct viscosity and translational diffusivity data at various temperature-pressure (
Language	English
Publishing date	2019-11-18
Publishing country	United States
Document type	Journal Article
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.9b08309
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Article: Understanding the Origin of the Breakdown of the Stokes–Einstein Relation in Supercooled Water at Different Temperature–Pressure Conditions

Dubey, Vikas / Erimban, Shakkira / Indra, Sandipa / Daschakraborty, Snehasis

Journal of physical chemistry. 2019 Nov. 08, v. 123, no. 47

2019

Abstract	A recent experiment has measured the viscosity of water down to approximately 244 K and up to 300 MPa. The correct viscosity and translational diffusivity data at various temperature–pressure (T–P) state points allowed for checking the validity of the Stokes–Einstein (SE) relation, which accounts for the coupling between translational self-diffusion and medium viscosity. The diffusion–viscosity decoupling increases with decreasing temperature, but the increasing pressure reduces the extent of the decoupling. Earlier simulation studies explained the breakdown of the SE relation in terms of the location of the Widom line, emanating from the liquid–liquid critical point (LLCP). Although these studies made a significant contribution to the current understanding of the above phenomena, a detailed molecular picture is still lacking. Recently, our group has explained the diffusion–viscosity decoupling from a jump-diffusion perspective. The jump-diffusion coefficient, emanating from the jump translation of water molecules, is calculated using a quantitative approach for different temperatures at ambient pressure. It has been observed that jump-diffusion is the key factor for diffusion–viscosity decoupling in supercooled water. The same method is adopted in the present work to estimate the jump-diffusion coefficient for different T–P state points and, thereby, explains the role of jump-diffusion for the different extents of the SE relation breakdown at different pressures. The residual diffusion coefficient, the other component of the total diffusion that originates from small step displacement and that is calculated by subtracting the jump-diffusion coefficient from the total diffusion, is seen to be fairly coupled to the viscosity at the entire range of temperature and pressure. Furthermore, we have calculated the average number of H-bonds per water molecule and the tetrahedral order for different T–P state points and investigated an approximate correlation between the average local structure and the contribution of the jump-diffusion to the total diffusion of water. This study, therefore, puts forward a new perspective for explaining the SE relation breakdown in supercooled water under different pressure conditions.
Keywords	ambient pressure ; diffusivity ; physical chemistry ; quantitative analysis ; temperature ; viscosity
Language	English
Dates of publication	2019-1108
Size	p. 10089-10099.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.9b08309
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Article: Influence of Coulombic Interaction on the Interfacial Self-Assembly of Discotic Liquid Crystal Amphiphiles: A Combined Experimental and Computer Simulation Study

Verma, Prakhar / Daschakraborty, Snehasis / Erimban, Shakkira / Kumar, Nishant / Kumar, Sandeep / Nayak, Alpana

Journal of physical chemistry. 2019 June 14, v. 123, no. 27

2019

Abstract: Self-assembly of amphiphilic molecules largely depends on the structure and electronic properties of the polar head groups. An important class of amphiphiles with technological applications comprises the discotic liquid crystal (DLC) amphiphiles. Here, ... ...

Abstract	Self-assembly of amphiphilic molecules largely depends on the structure and electronic properties of the polar head groups. An important class of amphiphiles with technological applications comprises the discotic liquid crystal (DLC) amphiphiles. Here, we report remarkable differences in the self-assembly properties of two similar discotic amphiphiles with dissimilar polar head groups, viz., imidazole-tethered with hexaalkoxytriphenylene (neutral-ImTp) and imidazolium-tethered with hexaalkoxytriphenylene (ionic-ImTp). Surface manometry reveals that the ionic-ImTp exhibits a larger limiting area, higher collapse pressure, and smaller compressional elastic modulus at the air–water interface as compared to the neutral-ImTp system. At the air–solid interface, ionic-ImTp can be transferred only up to a bilayer structure with undulated morphology, whereas the neutral-ImTp exhibits smooth morphology and higher transfer efficiency. These results are explained by density functional theory (DFT) calculations and molecular dynamics (MD) simulations, which elucidated that the Coulombic interaction is the dominant factor that controls the organization of these molecules. DFT calculations predicted a T-shaped π-stacking geometry for the ionic-ImTp and a parallel-displaced stacking geometry for the neutral-ImTp. MD simulation predicted the orientation of molecules and their strength of hydrogen bonding. Understanding the intermolecular interactions governing self-assembly is important to engineer molecular packing that controls the charge transport in DLC-based organic electronics.
Keywords	computer simulation ; density functional theory ; electronics ; geometry ; hydrogen bonding ; liquid crystals ; liquid-air interface ; modulus of elasticity ; molecular dynamics ; surfactants
Language	English
Dates of publication	2019-0614
Size	p. 16681-16689.
Publishing place	American Chemical Society
Document type	Article
ISSN	1932-7455
DOI	10.1021/acs.jpcc.9b02713
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