Yazan Haddad

12 Questions 36 Answers 0 Followers

Questions related from Yazan Haddad

Does anybody have experience with external GPU (eGPU) for molecular dynamics?

eGPU is quite portable and similar price to conventional graphics card. I am wondering if the CPU-GPU connection is fast enough to write down output on hard-disk and not make so big delay. My...

10 October 2018 621 3 View

How to use more CPUs in Sander module (in Amber software) as it is limited to number of residues in protein?

I am doing simulation for short peptides, which means that Sander module accepts limited number of CPUs for computation. I have learned that pmemd is limited to number of atoms (x10 the number of...

09 September 2017 4,731 3 View

Why is dissolved oxygen often neglected from molecular dynamics simulations in physiological conditions?

Unless doing a simulation of hemoglobin, I rarely see references to dissolved oxygen or carbon dioxide. Are they so much insignificant in biomolecule interactions?

03 March 2017 4,231 3 View

When two proteins bind together, what buried amino acid characteristics are an entropy advantage? and why?

I was reading that hidden surface with a lot of hydrophobic groups is considered an entropic advantage. To expand the question, is it entropic advantage when buried residues are long chained? Is...

02 February 2017 2,964 4 View

What is a minimium/representative number of protein structures (in PDB) to perform a study on a general structural characteristic?

For example, if we want to study frequency of a specific mutation (very common codon change) and its structural consequences. From an evolutionary or universal point of view, what is minimum...

01 January 2017 3,387 3 View

How does the impact factor change with increasing number of respected journals? should it decrease with time?

Since the impact factor indicates the citations of a respected journal, then with increasing number of journals shouldn't the citations be distributed somehow.. resulting in a decrease of impact...

06 June 2016 8,657 2 View

Does climate change affect the bioavailability of heavy metals in soil and water resources?

And which heavy metals are more susceptible to be affected?

04 April 2016 4,178 4 View

Simplified multiplication, how many solutions for N?

(X)(Y) = (N-X)(N-Y) + N(X+Y-N) This is representation of how we used to teach children multiplication on their ten fingers by overlapping two numbers from opposite sides and multiplying the...

01 January 2016 737 1 View

Any advice on Metallothioneins and Golgi aparatus?

Localization of Metallothionein at the Golgi membrane can support a hypothesis for a detoxification mechnasim throught secretion or exocytotic vesicles. Is there experimental data in the...

12 December 2015 2,463 1 View

What will happen if all papers submitted are published with reviewers opinions in footnotes?

As much as everyone complain from reviewers' comments, these can provide valuable information to researchers in general. Do you think reviewers (and editors) opinions will change if they knew they...

08 August 2015 527 6 View

How long do you think researchgate will survive without ads and sales representatives?

research websites related to troubleshooting is always a target for companies providing solutions. so far this website questions and answers are still based on solutions by concept rather than...

08 August 2015 4,172 0 View

How feasible is molecular dynamics simulation of a whole human body?

There are nearly 1000 trillion atoms per cell and nearly 37.2 trillion cells in the human body. However, coarse-grained simulation can reduce this significantly (arms and legs optional)?! Is the...

01 January 1970 7,489 3 View