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Article: Constraints on Knot Insertion, Not Internal Jamming, Control Polycatenane Translocation Dynamics through Crystalline Pores.

Wang, Zifeng / Ziolek, Robert M / Tsige, Mesfin

2023 Volume 56, Issue 8, Page(s) 3238–3245

Abstract: The translocation of polymers through pores and channels is an archetypal process in biology and is widely studied and exploited for applications in bio- and nanotechnology. In recent times, the translocation of polymers of various different topologies ... ...

Abstract	The translocation of polymers through pores and channels is an archetypal process in biology and is widely studied and exploited for applications in bio- and nanotechnology. In recent times, the translocation of polymers of various different topologies has been studied both experimentally and by computer simulation. However, in some cases, a clear understanding of the precise mechanisms that drive their translocation dynamics can be challenging to derive. Experimental methods are able to provide statistical details of polymer translocation, but computer simulations are uniquely placed to uncover a finer level of mechanistic understanding. In this work, we use high-throughput molecular simulations to reveal the importance that knot insertion rates play in controlling translocation dynamics in the small pore limit, where unexpected nonpower law behavior emerges. This work both provides new predictive understanding of polycatenane translocation and shows the importance of carefully considering the role of the definition of translocation itself.
Language	English
Publishing date	2023-04-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	3436-8
ISSN	0024-9297
ISSN	0024-9297
DOI	10.1021/acs.macromol.2c02565
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Article ; Online: Recent advancements in understanding the self-assembly of macroions in solution

Liu, Zhuonan / Qian, Kun / Liu, Tianbo / Tsige, Mesfin

Chemical communications (Cambridge, England)

2022 Volume 58, Issue 87, Page(s) 12151–12159

Abstract: Macroionic solutions behave quite differently from small ions in solution or colloids in suspension, representing a previously missing and very important transitional stage, and can further be connected to solutions of polyelectrolytes, including ... ...

Abstract	Macroionic solutions behave quite differently from small ions in solution or colloids in suspension, representing a previously missing and very important transitional stage, and can further be connected to solutions of polyelectrolytes, including proteins and DNA (
MeSH term(s)	Ions/chemistry ; Models, Molecular ; Colloids ; Proteins/chemistry
Chemical Substances	Ions ; Colloids ; Proteins
Language	English
Publishing date	2022-11-01
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/d2cc04535d
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Article ; Online: Adsorptive Structure and Mobility on Carbon Nanotube Exteriors Using Benzoic Acid as a Molecular Probe of Amphiphilic Water Contaminants.

Arsano, Iskinder / Talapatra, Saikat / Ma, Xingmao / Tsige, Mesfin

The journal of physical chemistry. B

2022 Volume 126, Issue 26, Page(s) 4956–4966

Abstract: Benzoic acid is the simplest aromatic carboxylic acid that is also a common water contaminant. Its structural and amphiphilic properties are shared by many other contaminants of concern. Based on a molecular dynamics study, this work reports the ... ...

Abstract	Benzoic acid is the simplest aromatic carboxylic acid that is also a common water contaminant. Its structural and amphiphilic properties are shared by many other contaminants of concern. Based on a molecular dynamics study, this work reports the competitive adsorption of benzoic acid with water on the curved exteriors of carbon nanotubes of varying oxygen content. With the help of cylindrically approximated pair correlation functions, carboxyl-carboxyl associations were found to serve as an additional mechanism providing stability to the adsorbed benzoic acid on tube exteriors. These associations are secondary to the main aromatic-aromatic interactions during the adsorption process and therefore were not sufficient to establish the energy hierarchy at the adsorbed state with increase in surface oxygen content. The same mechanism was previously ascribed to the adsorption of the structurally similar but bulkier tannic acid. Both water and benzoic acid were organized into numerous mobility groups and a correspondence was established between species residence time and the average translation time taken to escape the tube vicinity. Vigorous exchange of water molecules among the first adsorption shell, the second adsorption shell, and the immediate vicinity radially outside was estimated to take place within a short time of about 10 ps.
MeSH term(s)	Adsorption ; Benzoic Acid/chemistry ; Molecular Probes ; Nanotubes, Carbon/chemistry ; Oxygen ; Water/chemistry
Chemical Substances	Molecular Probes ; Nanotubes, Carbon ; Water (059QF0KO0R) ; Benzoic Acid (8SKN0B0MIM) ; Oxygen (S88TT14065)
Language	English
Publishing date	2022-06-24
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.2c01929
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Article ; Online: Molecular Dynamics Simulation of Entangled Melts at High Rates: Identifying Entanglement Lockup Mechanism Leading to True Strain Hardening.

Zheng, Yexin / Tsige, Mesfin / Wang, Shi-Qing

Macromolecular rapid communications

2022 , Page(s) e2200159

Abstract: In the present work, molecular dynamics simulations are carried out based on the bead-spring model to indicate how the entanglement lockup manifests in the late stage of fast Rouse-Weissnberg number ( ... ...

Abstract	In the present work, molecular dynamics simulations are carried out based on the bead-spring model to indicate how the entanglement lockup manifests in the late stage of fast Rouse-Weissnberg number (Wi
Language	English
Publishing date	2022-07-26
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1475027-2
ISSN	1521-3927 ; 1022-1336
ISSN (online)	1521-3927
ISSN	1022-1336
DOI	10.1002/marc.202200159
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Article: The “Raña” unit, an intensely weathered Late Neogene product from SW Iberia: Petrographic and geochemical evidences

Arribas, J / Garzón, G / Tejero, R / Tsige, M

Catena. 2021 Oct., v. 205

2021

Abstract: The Raña is a morphosedimentary unit related to the last record of the Guadiana Basin and located in the southwestern Iberian Peninsula. The Guadiana Basin is an intracratonic basin filled with <200 m of Paleogene and Neogene clastic sediments.The Raña ... ...

Abstract	The Raña is a morphosedimentary unit related to the last record of the Guadiana Basin and located in the southwestern Iberian Peninsula. The Guadiana Basin is an intracratonic basin filled with <200 m of Paleogene and Neogene clastic sediments.The Raña unit represents a relict unit that lies over the northern border of the Guadiana Basin and the Variscan basement of Neoproterozoic and Palaeozoic low-grade metasediments from the Iberian Massif. Raña deposits are alluvial fans abandoned by their feeding streams during the Late Neogene period. Outcrops correspond to the apex of the alluvial fans isolated from the fluvial network.This study analysed Raña deposits using petrographic, mineralogical, and geochemical techniques, which suggested a source-to-sink analysis by contrasting data among the three involved elements: source areas, basin fill sediments, and Raña deposits.Sandstones from the basin infill show primarily quartzolithic petrofacies as a consequence of the low-grade metamorphic character of the sources. The Raña sandstones show similar petrofacies with a greater quartz content than basin infill deposits and an important population of argillaceous pisoids. Kaolinite is the dominant clay mineral associated with the Raña units. The aforementioned characteristics indicate a sedimentary provenance from intensely weathered products. The contrast of the geochemical composition of the parent rocks, basin-fill, and Raña deposits also confirms the forced maturation of sediments by chemical weathering. Chemical index of alteration values show evolution from infill sediments (76) to Raña deposits (90) as a consequence of mobile cation loss (Ca, Na, and K). This approach is related to different zones of alteration in soils, suggesting the formation of sapropelic deposits on weathering mantles at the source under hot and wet climates (tropical) during the formation of the Raña deposits. Finally, the provenance signals prevail despite intense weathering.
Keywords	Neogene period ; Neoproterozoic era ; Paleogene period ; basins ; catenas ; cations ; clay ; evolution ; kaolinite ; provenance ; quartz ; Iberian Peninsula
Language	English
Dates of publication	2021-10
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	519608-5
ISSN	1872-6887 ; 0008-7769 ; 0341-8162
ISSN (online)	1872-6887 ; 0008-7769
ISSN	0341-8162
DOI	10.1016/j.catena.2021.105469
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Structure and Thermodynamics of Linear, Ring, and Catenane Polymers in Solutions and at Liquid-Liquid Interfaces.

Shandiz, Saeed Akbari / Leuty, Gary M / Guo, Hao / Mokarizadeh, Abdol Hadi / Maia, Joao M / Tsige, Mesfin

Langmuir : the ACS journal of surfaces and colloids

2023 Volume 39, Issue 20, Page(s) 7154–7166

Abstract: In recent decades, advances in the syntheses of mechanically interlocked macromolecules, such as catenanes, have led to much greater interest in the applications of these complexes, from molecular motors and actuators to nanoscale computational memory ... ...

Abstract	In recent decades, advances in the syntheses of mechanically interlocked macromolecules, such as catenanes, have led to much greater interest in the applications of these complexes, from molecular motors and actuators to nanoscale computational memory and nanoswitches. Much remains to be understood, however, regarding how catenated ring compounds behave as a result of the effects of different solvents as well as the effects of solvent/solvent interfaces. In this work, we have investigated, using molecular dynamics simulations, the effects of solvation of poly(ethylene oxide) chains of different topologies─linear, ring, and [2]catenane─in two solvents both considered favorable toward PEO (water, toluene) and at the water/toluene interface. Compared to ring and [2]catenane molecules, the linear PEO chain showed the largest increase in size at the water/toluene interface compared to bulk water or bulk toluene. Perhaps surprisingly, observations indicate that the tendency of all three topologies to extend at the water/toluene interface may have more to do with screening the interaction between the two solvents than with optimizing specific solvent-polymer contacts.
Language	English
Publishing date	2023-05-08
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.3c00589
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Article ; Online: Toward the Rational Design of Organic Solar Photovoltaics: Application of Molecular Structure Methods to Donor Polymers.

Mamba, Sandile / Perry, David S / Tsige, Mesfin / Pellicane, Giuseppe

The journal of physical chemistry. A

2021 Volume 125, Issue 50, Page(s) 10593–10603

Abstract: Conjugated polymers are promising candidates in the design of polymer solar cell materials with suitable electronic properties. Recent studies show that the use of different functional groups as side chain in thiophene-based polymers changes the ... ...

Abstract	Conjugated polymers are promising candidates in the design of polymer solar cell materials with suitable electronic properties. Recent studies show that the use of different functional groups as side chain in thiophene-based polymers changes the electronic and conformation structures. Here we design new thiophene-based molecules by replacing the hydrogen attached to the backbone of P3MT with electron-donating and electron-withdrawing groups. We then calculate the HOMO, LUMO, and HOMO-LUMO energy gap to quantify the theoretical merit of the new polymers as solar absorbers and their inter-ring torsional potential to understand their suitability to link together in high conductivity, extended conjugated systems. Calculations are done with first-principles density functional theory (DFT), implemented using B3LYP with dispersion function and 6-31G(d,p) as basis set. Our results show that the HOMO-LUMO gap is sensibly lowered by donating groups and we found that the substitution of the hydrogen with -NH
Language	English
Publishing date	2021-12-14
Publishing country	United States
Document type	Journal Article
ISSN	1520-5215
ISSN (online)	1520-5215
DOI	10.1021/acs.jpca.1c07091
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Article ; Online: Influence of Core Type and Shell Thickness on Avian-Inspired Structural Colors Produced from Melanin Nanoparticle Assemblies.

Singla, Saranshu / Yang, Zepeng / Patil, Anvay / Guo, Hao / Vanthournout, Bram / Htut, K Zin / Shawkey, Matthew D / Tsige, Mesfin / Dhinojwala, Ali

ACS applied materials & interfaces

2023 Volume 15, Issue 38, Page(s) 45229–45238

Abstract: Hollow melanosomes found in iridescent bird feathers, including violet-backed starlings and wild turkeys, enable the generation of diverse structural colors. It has been postulated that the high refractive index (RI) contrast between melanin (1.74) and ... ...

Abstract	Hollow melanosomes found in iridescent bird feathers, including violet-backed starlings and wild turkeys, enable the generation of diverse structural colors. It has been postulated that the high refractive index (RI) contrast between melanin (1.74) and air (1.0) results in brighter and more saturated colors. This has led to several studies that have synthesized hollow synthetic melanin nanoparticles and fabricated colloidal nanostructures to produce synthetic structural colors. However, these studies use hollow nanoparticles with thin shells (<20 nm), even though shell thicknesses as high as 100 nm have been observed in natural melanosomes. Here, we combine experimental and computational approaches to examine the influence of the varying polydopamine (PDA, synthetic melanin) shell thickness (0-100 nm) and core material on structural colors. Experimentally, a concomitant change in overall particle size and RI contrast makes it difficult to interpret the effect of a hollow or solid core on color. Thus, we utilize finite-difference time-domain (FDTD) simulations to uncover the effect of shell thickness and core on structural colors. Our FDTD results highlight that hollow particles with thin shells have substantially higher saturation than same-sized solid and core-shell particles. These results would benefit a wide range of applications including paints, coatings, and cosmetics.
Language	English
Publishing date	2023-09-12
Publishing country	United States
Document type	Journal Article
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.3c08152
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Article ; Online: Synergistic Effect of Physical and Chemical Cross-Linkers Enhances Shape Fidelity and Mechanical Properties of 3D Printable Low-Modulus Polyesters.

Ortiz-Ortiz, Deliris N / Mokarizadeh, Abdol Hadi / Segal, Maddison / Dang, Francis / Zafari, Mahdi / Tsige, Mesfin / Joy, Abraham

Biomacromolecules

2023 Volume 24, Issue 11, Page(s) 5091–5104

Abstract: Three-dimensional (3D) printing is becoming increasingly prevalent in tissue engineering, driving the demand for low-modulus, high-performance, biodegradable, and biocompatible polymers. Extrusion-based direct-write (EDW) 3D printing enables printing and ...

Abstract	Three-dimensional (3D) printing is becoming increasingly prevalent in tissue engineering, driving the demand for low-modulus, high-performance, biodegradable, and biocompatible polymers. Extrusion-based direct-write (EDW) 3D printing enables printing and customization of low-modulus materials, ranging from cell-free printing to cell-laden bioinks that closely resemble natural tissue. While EDW holds promise, the requirement for soft materials with excellent printability and shape fidelity postprinting remains unmet. The development of new synthetic materials for 3D printing applications has been relatively slow, and only a small polymer library is available for tissue engineering applications. Furthermore, most of these polymers require high temperature (FDM) or additives and solvents (DLP/SLA) to enable printability. In this study, we present low-modulus 3D printable polyester inks that enable low-temperature printing without the need for solvents or additives. To maintain shape fidelity, we incorporate physical and chemical cross-linkers. These 3D printable polyester inks contain pendant amide groups as the physical cross-linker and coumarin pendant groups as the photochemical cross-linker. Molecular dynamics simulations further confirm the presence of physical interactions between different pendants, including hydrogen bonding and hydrophobic interactions. The combination of the two types of cross-linkers enhances the zero-shear viscosity and hence provides good printability and shape fidelity.
MeSH term(s)	Polyesters ; Bioprinting/methods ; Rheology ; Tissue Engineering ; Printing, Three-Dimensional ; Polymers ; Solvents ; Tissue Scaffolds/chemistry
Chemical Substances	Polyesters ; Polymers ; Solvents
Language	English
Publishing date	2023-10-26
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ISSN	1526-4602
ISSN (online)	1526-4602
DOI	10.1021/acs.biomac.3c00684
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Article ; Online: Multiphasic Coacervates Assembled by Hydrogen Bonding and Hydrophobic Interactions.

Liu, Xinhao / Mokarizadeh, Abdol Hadi / Narayanan, Amal / Mane, Prathamesh / Pandit, Avanti / Tseng, Yen-Ming / Tsige, Mesfin / Joy, Abraham

Journal of the American Chemical Society

2023 Volume 145, Issue 42, Page(s) 23109–23120

Abstract: Coacervation has emerged as a prevalent mechanism to compartmentalize biomolecules in living cells. Synthetic coacervates help in understanding the assembly process and mimic the functions of biological coacervates as simplified artificial systems. ... ...

Abstract	Coacervation has emerged as a prevalent mechanism to compartmentalize biomolecules in living cells. Synthetic coacervates help in understanding the assembly process and mimic the functions of biological coacervates as simplified artificial systems. Though the molecular mechanism and mesoscopic properties of coacervates formed from charged coacervates have been well investigated, the details of the assembly and stabilization of nonionic coacervates remain largely unknown. Here, we describe a library of coacervate-forming polyesteramides and show that the water-tertiary amide bridging hydrogen bonds and hydrophobic interactions stabilize these nonionic, single-component coacervates. Analogous to intracellular biological coacervates, these coacervates exhibit "liquid-like" features with low viscosity and low interfacial energy, and form coacervates with as few as five repeating units. By controlling the temperature and engineering the molar ratio between hydrophobic interaction sites and bridging hydrogen bonding sites, we demonstrate the tuneability of the viscosity and interfacial tension of polyesteramide-based coacervates. Taking advantage of the differences in the mesoscopic properties of these nonionic coacervates, we engineered multiphasic coacervates with core-shell architectures similar to those of intracellular biological coacervates, such as nucleoli and stress granule-p-body complexes. The multiphasic structures produced from these synthetic nonionic polyesteramide coacervates may serve as a valuable tool for investigating physicochemical principles deployed by living cells to spatiotemporally control cargo partitioning, biochemical reaction rates, and interorganellar signal transport.
MeSH term(s)	Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Temperature ; Water/chemistry
Chemical Substances	Water (059QF0KO0R)
Language	English
Publishing date	2023-10-11
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.3c06675
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