- Albert Einstein-

“Things should be made as simple as possible,
but not any simpler."

https://web.njit.edu/~cld/papers/JALA23.pdf

Sharareh Jalali, Ruoyao Zhang, Mikko P. Haataja, and Cristiano L. Dias, Nucleation and Growth of Amyloid Fibrils, J. Phys. Chem. B 127:45, 9759–9770 (2023).

Yanxing Yang and Cristiano L. Dias, Peptide−Membrane Binding: Effects of the Amino Acid Sequence, J. Phys. Chem. B 127, 912−920 (2023).

Yanxing Yang, Hannah Distaffen, Sharareh Jalali, Andrew J. Nieuwkoop, Bradley L. Nilsson, and Cristiano L. Dias, Atomic Insights into Amyloid-Induced Membrane Damage, ACS Chem. Neurosci. 13:2766 (2022).

Sharareh Jalali, Yanxing Yang, Farbod Mahmoudinobar, Shaneen M. Singh, Bradley L. Nilsson, and Cristiano Dias, Using all-atom simulations in explicit solvent to study aggregation of amphipathic peptides into amyloid-like fibrils, J. Mol. Liq. 347:18283 (2022).

Yanxing Yang, Sharareh Jalali, Bradley L. Nilsson, and Cristiano L. Dias, Binding Mechanisms of Amyloid-like Peptides to Lipid Bilayers and Effects of Divalent Cations, ACS Chem. Neurosci. 12:2027–2035 (2021).

Zhaoqian Su, Saman Alavi, John A. Ripmeester, Gedaliah Wolosh, and Cristiano L. Dias, Methane Clathrate Formation is Catalyzed and Kinetically Inhibited by the Same Molecule: Two Facets of Methanol, J. Phys. Chem. B 125, 4162-4168 (2021).

Farbod Mahmoudinobar, Bradley L. Nilsson, and Cristiano L. Dias, Effects of Ions and Small Compounds on the Structure of Aβ42 Monomers, Phys. Chem. B 125, 4, 1085–1097 (2021).

Cristiano L. Dias, Sharareh Jalali, Yanxing Yang, and Luis Cruz, Role of Cholesterol on Binding of Amyloid Fibrils to Lipid Bilayers, J. Phys. Chem. B 124:3036-3042 (2020).

Zhaoqian Su and Cristiano Dias, Individual and combined effects of urea and trimethylamine N-oxide (TMAO) on protein structures, Journal of Molecular Liquids, 293, 111443 (2019).

Farbod Mahmoudinobar and Cristiano Dias, GRADE: A Code to Determine Clathrate Hydrate Structures, accepted for publication in Computer Physics Communications 244:385 (2019).

Farbod Mahmoudinobar, Jennifer Urban, Zhaoqian Su, Bradley Nilsson, and Cristiano Dias, Thermodynamic stability of polar and non-polar amyloid fibrils, Journal of Chemical Theory and Computation 15, 3868 (2019).

Young M. Jeong, Cristiano Dias, Casey Diekman, Helene Brochon, Pyonghwa Kim, Manpreet Kaura, Yong-Sung Kim, Hye-In Jang, Yong-Ick Kim, Magnesium regulates the circadian oscillator in cyanobacteria, Journal of Biological Rhythms 34, 380 (2019).

Tomaz Urbic and Cristiano L. Dias, Thermodynamic properties of amyloid fibrils: A simple model of peptide aggregation, Fluid Phase Equilibria 489, 104 (2019).

J.S.Espinoza Ortiz, and C.L.Dias, Cooperative fibril model: Native, amyloid-like fibril, and unfolded states of proteins, Physica A 511, 154–165 (2018).

Zhaoqian Su, Gopal Ravindhran, and Cristiano Dias, Effects of Trimethylamine-N-oxide (TMAO) on hydrophobic and charged interactions, J. Phys. Chem. B 122, 5557 (2018).

Zhaoqian Su, Farbod Mahmoudinobar, and Cristiano Dias, Role of TMAO on the conformation of peptides and its implication for proteins, Phys. Rev. Letters 119, 108102 (2017), Editor's suggestion.

Zhaoqian Su and Cristiano L. Dias, Molecular mechanism of protein unfolding by urea, Journal of Molecular Liquids 228, 168-175 (2017).

Tomaz Urbic, Sara Nadem and Cristiano L. Dias, Thermodynamic properties of amyloid fibrils in equilibrium, Biophysical Chemistry 231,155 (2017).

Srinivasa R. Jampani, Farbood Mahmoudinobar, Zhaoqian Su and Cristiano L. Dias, Thermodynamics of Abeta16-21 dissociation from a fibril, PROTEIN: Structure, Function, and Bioinformatics 83:1963–1972 (2015).

Farbood Mahmoudinobar, Cristiano L. Dias*, and Ronen Zangi, Role of side-chain interactions on the formation of alpha-helices in model peptides, Phys. Rev. E 91, 032710 (2015).

Cristiano L. Dias and Hue Sun Chan. Pressure-Dependence Properties of Elementary Hydrophobic Interactions: Ramifications for Activation Properties of Protein Folding. J. Phys. Chem. B 118 , 7488 (2014).

Tomaz Urbic and Cristiano L. Dias. Hydration of non-polar anti-parallel beta-sheets. J. Chem. Phys. 140, 165101 (2014).

Tomaz Urbic and Cristiano L. Dias. Properties of Lennard-Jones dimeric fluid in two dimensions: An integral equation study. J. Chem. Phys. 140, 094703 (2014).

Chitra Narayanan and Cristiano L. Dias. Exploring the free energy landscape of a model beta-hairpin peptide and its isoform. PROTEIN: Structure, Function, and Bioinformatics 82, 2394 (2014).

Zhaoqian Su and Cristiano L. Dias. Driving beta-strands into fibrils. J. Phys. Chem. B 118, 10830 (2014).

Chitra Narayanan and Cristiano L. Dias. Hydrophobic interactions and hydrogen bonds in beta-sheet formation. J. Chem. Phys. 139, 115103 (2013).

Cristiano L. Dias. Unifying microscopic mechanism for pressure and cold denaturations of proteins, Physical Review letter 109, 048104 (2012) [supplemental material].

T. Hynninen, C.L. Dias, A. Mkrtchyan, V. Heinonen, M. Karttunen, A.S. Foster, and T. Ala-Nissila. A molecular dynamics implementation of the 3D Mercedes-Benz water model, Computer Physics Communication 183, 363 (2012).

Cristiano L. Dias, Mikko Karttunen and Hue Sun Chan. Hydrophobic interactions in the formation of secondary structures in small peptides, Physical Review E 84, 041931 (2011).

Cristiano L. Dias, Teemu Hynninen, Tapio Ala-Nissila, Adam S. Foster and Mikko Karttunen. Hydrophobicity within the three-dimensional Mercedes-Benz model: Potential of mean force, J. Chem. Phys. 134, 65106 (2011).

Teemu Hynninen, Vili Heinonen, Cristiano L. Dias, Mikko Karttunen, Adam S. Foster and Tapio Ala-Nissila. Cutting Ice: Nanowire Regelation, Physical Review Letters 105, 086102 (2010).

See also Physorg.

Jirasak Wong-Ekkabut, M. Miettinen, Cristiano L. Dias and Mikko Kartunnen. Static charges cannot drive a continuous flow of water molecules through a carbon nanotube, Nature Nanotechnology 5, 555 (2010).

Cristiano L. Dias, Tapio Ala-Nissila, Jirasak Wong-ekkabut, Ilpo Vattulainen, Martin Grant and Mikko Karttunen. Reply to the comment by Graziano on The hydrophobic effect and its role in cold denaturation, Cryobiology 60, 356 (2010).

Cristiano L. Dias, Tapio Ala-Nissila, Jirasak Wong-ekkabut, Ilpo Vattulainen, Martin Grant and Mikko Karttunen. The hydrophobic effect and its role in cold denaturation. Cryobiology 60, 91 (2010).

Cristiano L. Dias, Jens Kroger, Daniel Vernon and Martin Grant. Nucleation of cracks in a brittle sheet. Physical Review E 80, 066109 (2009).

Cristiano L. Dias, Tapio Ala-Nissila, Martin Grant and Mikko Karttunen. Three-dimensional "Mercedes-Benz" model for water. J. Chem. Phys. 131, 054505 (2009).

Xavier Urli, Cristiano L. Dias, Laurent J. Lewis, and Sjoerd Roorda. Point defects in pure amorphous silicon and their role in structural relaxation: A tight-binding molecular-dynamics study. Physical Review B 77, 155204 (2008).

Cristiano L. Dias, Tapio Ala-Nissila, Mikko Karttunen, Ilpo Vattulainen, and Martin Grant. Microscopic mechanism for cold denaturation. Physical Review Letters 100, 118101 (2008).

Anirban Sain, Cristiano L. Dias, and Martin Grant. Rupture of an extended object: A many-body Kramers calculation. Physical Review E 74, 046111 (2006).

C. L. Dias and Martin Grant. Unfolding designable structures. The European Physical Journal B 50, 265 (2006).

Cristiano L. Dias and Martin Grant. Designable structures are easy to unfold. Physical Review E 74, 042902 (2006).

Cristiano L. Dias, Martin Dube, Fernando Oliveira, and Martin Grant. Scaling in Force Spectroscopy. Physical Review E 72, 011918 (2005).

Warin Rangubpit, Siwaporn Sungted, Jirasak Wong-Ekkabut, Hannah E Distaffen, Bradley L Nilsson, Cristiano L Dias, Pore Formation by Amyloid-like Peptides: Effects of the Nonpolar–Polar Sequence Pattern, ACS Chem. Neurosci. 15:3354 (2024)

Phansiri Boonnoy, Minchakarn Janlad, Behnaz Bagheri, Cristiano Dias, Mikko Karttunen and Jirasak Wong-ekkabut, Cholesterol inhibits oxygen permeation through biological membranes: mechanism against double-bond peroxidation, RSC Adv., 14:29113 (2024).

Peter Ogrin, Cristiano L. Dias, Tomaz Urbic, Code for molecular dynamics simulation of two dimensional
Mercedes-Benz water model, Computer Physics Communications 303:109267 (2024).

N. Nisoh, V. Jarerattanachat,C. Dias and J. Wong-Ekkabut, Insight into the interactions of fullerenes with biological membranes through molecular dynamics simulations, Advances in Physics X 9:1–19 (2024).

Bradley L. Nilsson, Gizem Celebi Torabfam, and Cristiano L. Dias, Peptide Self-Assembly into Amyloid Fibrils: Unbiased All-Atom Simulations, J. Phys. Chem. B 128:3320–3328 (2024).

Ruoyao Zhang, Sharareh Jalali, Cristiano L. Dias, and Mikko P. Haataja, Growth kinetics of amyloid-like fibrils: An integrated atomistic simulation and continuum theory approach, PNAS Nexus, 3:1–12 (2024).

- Albert Einstein-

“Things should be made as simple as possible, but not any simpler."

Publications

“Things should be made as simple as possible,
but not any simpler."